Supplementary Table 3
Summary of genomic annotation by HaploReg v2 and RegulomeDB. Data are shown for GWAS hits and proxy SNPs (r 2>0.4 in
1000Genomes EUR phase 1 data) demonstrating evidence of histone marks, DNAse hypersensitivity sites or transcription factor occupancy in HaploReg v2
analysis. Also indicated are GERP scores>2 and RegulomeDB scores for all SNPs.
(a) 3q28
LD LD
chr pos (hg19) (r²)2 (D')2
variant1
Ref Alt
3 189 301 627 0.52 0.83 rs73188250 C T
3 189 302 969 0.52 0.83 rs3922955 A G
AFR
freq
0.02
0.02
AMR
freq
0.27
0.27
ASN
freq
0.31
0.31
EUR GERP
freq cons3
0.42
0.42
189 303 627
3
0.52 0.83 rs17443378
C
G
0.02 0.27 0.31 0.42
0.51
0.58
0.57
0.53
0.52
0.52
0.49
0.45
0.59
0.63
0.59
0.95
0.41
0.64
0.6
0.56
0.56
0.6
0.41
0.65
0.42
0.65
0.65
189 303 679
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
C
T
A
A
G
A
C
G
A
T
C
A
A
G
T
G
C
G
T
G
A
C
C
T
G
G
G
A
C
T
T
G
A
A
G
G
A
G
T
G
A
A
A
G
T
T
0.24
0.4
0.39
0.54
0.25
0.16
0.23
0.19
0.23
0.22
0.23
0.28
0.07
0.22
0.26
0.13
0.13
0.52
0.07
0.3
0.07
0.3
0.21
0.43 0.99
rs4687079
G
A
0.6 0.65 0.99 0.69
0.99 0.99 rs55779747
189 354 741 0.59 -0.99 rs11720249
189 356 221 0.66 0.99 rs4396880
189 356 261 0.98 0.99 rs4488809
A
C
G
T
C
T
A
C
0.32
0.16
0.29
0.34
0.37
0.48
0.28
0.38
0.53
0.05
0.33
0.52
0.49
0.38
0.39
0.49
H1
GM12878
GM12878
GM12878
A
G
T
A
G
A
C
G
0.29
0.28
0.28
0.33
0.28
0.28
0.28
0.38
0.33
0.32
0.33
0.53
0.39
0.39
0.39
0.49
GM12878
GM12878
GM12878
GM12878
189 354 127
189 356 598
0.66 0.99
189 356 665 0.66 0.99
189 356 675 0.66 0.99
189 356 941 0.99 0.99
rs4381914
rs4396881
rs4327365
rs7636839
0.39
0.59
0.59
0.61
0.39
0.38
0.39
0.35
0.4
0.39
0.4
0.49
0.31
0.39
0.41
0.38
0.38
0.6
0.31
0.39
0.31
0.39
0.39
HMEC, NHEK
NHEK,
GM12878,
HMEC
NHEK,
GM12878,
HMEC
rs9849804
rs6444389
rs1920288
rs9822622
rs73194153
rs4687073
rs9812901
rs1920286
rs56260952
rs9825172
rs9881000
rs36108040
rs73194157
rs28632188
rs34566957
rs9827043
rs7622692
rs10937396
rs9857400
rs9332461
rs9879817
rs4398410
rs9835951
189 354 012
0.07
0.97
0.96
0.97
0.03
0.03
0.39
0.44
0.35
0.32
0.35
0.52
0.01
0.32
0.41
0.03
0.03
0.64
0.01
0.32
0.01
0.33
0.32
Enhancer
histone marks
-0.92
0.93
0.92
0.94
-0.93
-0.94
0.86
0.9
0.92
0.97
0.92
0.98
-0.97
0.98
-0.95
-0.97
-0.97
-0.92
-0.97
0.99
-0.98
0.99
0.99
189 323 685
189 325 289
189 326 046
189 327 230
189 327 405
189 331 804
189 333 335
189 334 966
189 335 242
189 335 606
189 335 844
189 336 475
189 337 839
189 339 311
189 339 497
189 340 241
189 341 297
189 341 516
189 341 790
189 342 181
189 344 011
189 346 567
0.49
0.46
0.46
0.49
0.48
0.47
0.29
0.31
0.32
0.29
0.32
0.38
0.32
0.28
0.36
0.48
0.48
0.65
0.31
0.28
0.31
0.28
0.28
Promoter
histone
marks
DNAse5
Proteins
bound
eQTL
tissues
RefSeq genes
48kb 5' of TP63
46kb 5' of TP63
GLI,NF-I,Pbx3
46kb 5' of TP63
7
Foxp1,HDAC2,SETDB1
5 altered motifs
7 altered motifs
Rhox11
8 altered motifs
RBP-Jkappa,SRF
CIZ,Fox,HNF4
7 altered motifs
AP-1,Rad21,STAT
Cdc5,Nkx2
5 altered motifs
CEBPG
16 altered motifs
46kb 5' of TP63
26kb 5' of TP63
24kb 5' of TP63
23kb 5' of TP63
22kb 5' of TP63
22kb 5' of TP63
17kb 5' of TP63
16kb 5' of TP63
14kb 5' of TP63
14kb 5' of TP63
14kb 5' of TP63
13kb 5' of TP63
13kb 5' of TP63
11kb 5' of TP63
9.9kb 5' of TP63
9.7kb 5' of TP63
9kb 5' of TP63
7.9kb 5' of TP63
7.7kb 5' of TP63
7.4kb 5' of TP63
7kb 5' of TP63
5.2kb 5' of TP63
2.6kb 5' of TP63
6
5
6
7
6
7
6
6
5
7
7
7
6
7
6
6
6
7
7
5
5
7
6
Egr-1,p300
TP63
intronic
5
5 altered motifs
6 altered motifs
AP-2
8 altered motifs
AP-1,EWSR1FLI1,HDAC2
4 altered motifs
4 altered motifs
4 altered motifs
TP63
TP63
TP63
TP63
intronic
intronic
intronic
intronic
5
6
5
5
TP63
TP63
TP63
TP63
intronic
intronic
intronic
intronic
5
5
5
6
HRPEpiC
GATA
5 altered motifs
Foxa
Spz1
4 altered motifs
Cdx,Mef2,TATA
AIRE,HMG-IY
5 altered motifs
HMEC
GM12878
SK-N-MC
Th2
GM12878
GM12878, H1
WERI-Rb1
WERI-Rb1
GM12864
GM12864
MAFK
MAFK
MAFK
ReguomeDB4
Motifs changed
7 altered motifs
HEEpiC
Osteobl
dbSNP
func
annot
6
5
chr
3
3
3
3
3
pos (hg19)
189 357 199
189 357 602
189 357 616
189 357 861
189 358 698
LD LD
(r²)2 (D')2
1
1
1
1
1
1
0.44 -1
0.66 1
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
189 359 836
189 360 235
189 360 406
189 361 400
189 362 620
189 363 001
189 363 999
189 364 094
189 364 424
189 365 424
189 365 491
189 365 570
189 366 595
189 366 763
189 366 979
189 367 034
189 367 116
189 367 352
189 367 551
189 368 097
189 368 255
189 368 357
189 368 424
189 368 425
189 368 425
189 368 648
189 368 962
189 369 052
189 369 390
189 369 843
189 370 705
189 370 780
189 371 014
189 371 811
189 372 363
189 372 997
189 373 185
189 373 991
189 376 016
189 376 305
0.99
0.99
0.98
0.98
0.58
0.45
0.54
0.52
0.54
0.67
0.66
0.66
0.8
0.8
0.55
0.4
0.56
0.67
0.67
0.55
0.8
0.8
0.43
0.4
0.42
0.55
0.51
0.49
0.51
0.51
0.54
0.5
0.41
0.67
0.42
0.67
0.41
0.65
0.41
0.65
3
3
3
189 376 356 0.65 0.99 rs9835487
189 378 556 0.96 0.98 rs1920272
189 379 290 0.57 -0.97 rs13321778
0.99
0.99
0.99
0.99
0.89
0.81
0.84
0.81
0.85
0.98
-0.98
-0.98
-0.98
-0.98
0.86
-0.67
0.86
-0.98
-0.98
0.86
-0.98
-0.98
-0.68
-0.64
-0.68
0.86
-0.8
-0.78
-0.8
-0.8
0.85
-0.79
0.67
-0.97
-0.98
-0.97
0.67
0.99
0.67
0.99
AFR
variant1
Ref Alt freq
rs13080835 G T 0.33
rs13314271 T C 0.33
rs12696594 A G 0.33
rs73194170 A C 0.07
rs13325621 C T 0.28
rs55862124
rs7619517
rs7629983
rs13084874
rs9837544
rs9842008
rs9827354
rs9827487
rs9827991
rs1920235
rs4687080
rs4687081
rs9811174
rs9811214
rs6807954
rs13088465
rs6808068
rs28612247
rs17504410
rs8179917
rs9821164
rs4426661
rs4011820
rs200036880
rs4011821
rs6772378
rs12330526
rs10937398
rs9826717
rs12330765
rs9869716
rs1920271
rs1920266
rs1881992
rs9862450
rs9847400
rs9847745
rs1920248
rs9872452
rs4362700
AMR
freq
0.38
0.38
0.38
0.32
0.28
ASN
freq
0.53
0.53
0.53
0.01
0.32
EUR GERP
freq cons3
0.49
0.49
0.49
0.31
0.39
T C 0.33 0.38 0.53 0.49
T C 0.33 0.38 0.53 0.49
A G 0.25 0.38 0.53 0.49
T C 0.33 0.38 0.53 0.49
T C 0.28 0.29 0.33 0.41
T C 0.25 0.29 0.31 0.4
C T 0.35 0.33 0.6 0.43
C A 0.35 0.33 0.59 0.43
C T 0.34 0.29 0.55 0.42
A G 0.44 0.46 0.91 0.58
G A 0.17 0.5 0.09 0.42
G A 0.17 0.5 0.09 0.41
G A 0.19 0.53 0.09 0.46
C T 0.19 0.53 0.09 0.46
A T 0.25 0.29 0.54 0.42
T C 0.24 0.63 0.45 0.53
A G 0.35 0.29 0.54 0.42
C A 0.17 0.5 0.09 0.42
C T 0.17 0.5 0.09 0.42
C A 0.1 0.27 0.54 0.42
G A 0.19 0.53 0.09 0.46
T A 0.19 0.53 0.09 0.46
A T 0.23 0.59 0.38 0.53
G GTT 0.21 0.59 0.36 0.52
G T 0.22 0.59 0.38 0.53
G A 0.34 0.29 0.54 0.42
T C 0.25 0.63 0.4 0.57
G A 0.25 0.63 0.4 0.56
G A 0.25 0.63 0.4 0.57
A T 0.25 0.63 0.4 0.57
A G 0.35 0.3 0.54 0.42
G A 0.25 0.62 0.4 0.56
C A 0.47 0.33 0.72 0.47
G T 0.16 0.51 0.05 0.42
T C 0.07 0.31 0.01 0.31
G T 0.16 0.51 0.05 0.42
G A 0.47 0.34 0.72 0.47
T A 0.2 0.28 0.33 0.39
A G 0.47 0.33 0.72 0.47
A G 0.28 0.28 0.33 0.39
C
A
C
T
G
G
0.28 0.28 0.33 0.39
0.33 0.38 0.52 0.49
0.15 0.48 0.05 0.38
Promoter
histone
marks
Enhancer
histone marks DNAse5
GM12878
GM06990
GM12878,
HMEC
4 cell
types
Proteins
bound
ERALPHA_A
eQTL
tissues
Motifs changed
5 altered motifs
4 altered motifs
5 altered motifs
4 altered motifs
4 altered motifs
RefSeq genes
TP63
TP63
TP63
TP63
TP63
4 altered motifs
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
TP63
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
4
7
7
7
7
7
7
7
6
6
7
7
6
7
6
7
6
7
7
6
6
6
6
6
6
7
7
6
6
5
6
6
7
7
6
7
6
7
6
7
TP63
TP63
TP63
intronic
intronic
intronic
7
7
7
6 altered motifs
4 altered motifs
PLZF
Mef2,PLZF,Pax-4
4 altered motifs
6 altered motifs
Hoxa5
Pbx-1
4 altered motifs
Duxl,Hlx1
10 altered motifs
BRCA1,Pou2f2,Pou3f2
4 altered motifs
4 altered motifs
BATF,Irf
11 altered motifs
4 altered motifs
Nanog,TATA,p300
HNF4,THAP1
4 altered motifs
HNF4
Foxa,STAT
5 altered motifs
GCNF,LBP-9,Zfx
CTCF
p53
GR,SIX5,Zbtb12
19 altered motifs
BAF155
GM12878
GM12878
GM12878
GM12878
dbSNP
func
annot ReguomeDB4
intronic
5
intronic
7
intronic
6
intronic
6
intronic
6
7 altered motifs
5 altered motifs
4 altered motifs
4 altered motifs
Dobox4,Sin3Ak20,TCF4
chr
3
3
3
3
3
3
3
pos (hg19)
189 379 493
189 379 524
189 380 470
189 380 483
189 380 563
189 380 707
189 381 256
LD
(r²)2
0.67
0.57
0.67
0.67
0.67
0.67
0.66
LD
(D')2
-0.97
-0.97
-0.97
-0.97
-0.97
-0.97
0.99
AFR
variant1
Ref Alt freq
rs1920273 G A 0.16
rs1920274 A G 0.15
rs73194199 C A 0.16
rs73195959 G A 0.16
rs73195961 G A 0.16
rs73195962 G T 0.16
rs62291707 G A 0.28
AMR
freq
0.5
0.48
0.5
0.5
0.5
0.5
0.28
ASN
freq
0.05
0.05
0.05
0.05
0.05
0.05
0.33
EUR GERP
freq cons3
0.42
0.38
0.42
0.42
0.42
0.42
0.39
Promoter
histone
marks
Enhancer
histone marks
GM12878
GM12878
HSMM, NHLF,
HMEC
NHEK, HMEC,
HSMM
NHEK, HSMM,
GM12878
3
189 382 083 0.57 -0.97 rs10937404
G
A
0.15 0.48 0.05 0.38
3
189 383 093 0.42 -0.97
G
A
0.07 0.31 0.01 0.32
3
3
3
3
3
3
189 383 183
189 383 538
189 384 367
189 385 947
189 388 865
189 389 076
T
G
G
T
G
T
0.31
0.29
0.07
0.28
0.28
0.31
3
3
C
A
A
C
C
G
AA
AG
189 390 410 0.65 0.93 rs138906960 G
189 390 700 0.63 0.97 rs6794898 G
A
C
0.36 0.37 0.45 0.42
0.29 0.29 0.33 0.39
GM12878
GM12878
3
3
189 391 592 0.41 0.68 rs13085052
189 392 057 0.42 0.68 rs1920282
G
G
0.47 0.33 0.72 0.46
0.47 0.33 0.72 0.46
GM12878
GM12878
0.5
0.63
0.41
0.64
0.63
0.49
rs9872590
0.8 rs10937405
0.97 rs2378507
-0.97 rs10154920
0.98 rs9985415
0.97 rs4011816
0.79 rs3954248
T
A
0.31
0.29
0.32
0.28
0.28
0.31
0.33
0.33
0.01
0.33
0.33
0.33
0.43
0.39
0.32
0.39
0.39
0.43
DNAse5
Proteins
bound
SK-N-MC
SK-N-MC
GM18507
,SK-N-MC
5 bound
proteins
eQTL
tissues
Motifs changed
Smad
Hand1,Hoxd10,Irf
10 altered motifs
16 altered motifs
Hoxb13,Ik-2,TATA
PLAG1,STAT
Evi-1,STAT
RefSeq genes
TP63
TP63
TP63
TP63
TP63
TP63
TP63
dbSNP
func
annot
intronic
intronic
intronic
intronic
intronic
intronic
intronic
CEBPG,Pou2f2,STAT
TP63
intronic
5
5 altered motifs
TP63
intronic
7
Evi-1,Myc
12 altered motifs
PRDM1,p300
Irf
NRSF
Foxp1,Pax-4
TP63
TP63
TP63
TP63
TP63
TP63
intronic
intronic
intronic
intronic
intronic
intronic
5
6
7
7
6
7
9 altered motifs
STAT,TLX1::NFIC
TP63
TP63
intronic
intronic
3b
2b
Irf,Sox
BCL,LBP-9
TP63
TP63
intronic
intronic
3a
5
ReguomeDB4
7
7
7
6
6
7
7
(b) 5q15.33
chr
pos (hg19)
LD LD
(r²)2 (D')2
AFR AMR ASN EUR GERP
Ref Alt freq freq freq freq cons3
5
1 282 319
0.46 -0.95
5
5
5
5
5
1 282 414
1 283 312
1 284 135
1 285 162
1 285 974
0.5
0.5
0.45
0.44
0.45
5
5
5
1 286 516
1 287 194
1 287 340
1
1
0.46 0.83
0.43 0.91
chr
pos (hg19)
LD LD
(r²)2 (D')2
variant1
5
1 306 521
0.42 0.8
rs7446461
G
C
0.02 0.1 0.12 0.17
5
1 308 552
0.44 0.75
rs4635969
G
A
0.34 0.13 0.12 0.2
5
1 312 329
0.68 0.92 rs35953391
C
T
0.03 0.1 0.12 0.2
variant1
rs7726159
C
A
0.19 0.36 0.36 0.34
-0.95 rs7725218
0.71 rs7713218
-0.94 rs4449583
0.7 rs10866498
-0.98 rs7705526
G
A
C
C
C
A
G
T
T
A
0.43
0.56
0.18
0.33
0.18
C
G
A
A
A
G
0.57 0.55 0.61 0.5
0.71 0.65 0.67 0.6
0.84 0.69 0.62 0.66
rs2736100
rs2853677
rs2736099
0.39
0.54
0.35
0.51
0.31
0.36
0.61
0.35
0.59
0.37
Promoter
histone
marks
Enhancer
histone marks
0.36
0.5
0.33
0.47
0.32
AFR AMR ASN EUR GERP
Ref Alt freq freq freq freq cons3
Promoter
histone
marks
Enhancer
histone marks
RefSeq genes
GR,Myf
TERT
intronic
5
4 altered motifs
YY1
7 altered motifs
NRSF,Pax-6
6 altered motifs
TERT
TERT
TERT
TERT
TERT
intronic
intronic
intronic
intronic
intronic
5
5
5
5
7
Foxa
TERT
TERT
TERT
intronic
intronic
intronic
5
5
5
DNAse5
Proteins
bound
eQTL
tissues
dbSNP
func
annot
ReguomeDB4
Motifs changed
GM12878
G
C
0.03 0.1 0.12 0.2
GM12878
5
5
1 317 481
1 319 680
0.77 0.91 rs13170453
0.74 0.92 rs451360
A
C
G
A
0.02 0.14 0.12 0.22
0.02 0.14 0.12 0.22
GM12878
intronic
7
5
5
1 328 897
0.79 0.92
T
0.02 0.14 0.12 0.23
5 cell types
5
1 335 385
C
0.02 0.14 0.12 0.22
5
1 335 390
C
CT
0.82 0.95 rs3030832 G
TG
0.83 0.95 rs200350933 G
CLPTM1L
intronic
4
5 altered motifs
CLPTM1L
intronic
5
T
0.02 0.14 0.12 0.22
8 altered motifs
CLPTM1L
1.1kb 5' of
CLPTM1L
intronic
5
5 altered motifs
22 cell
types
7 cell
types
5
1 346 081
0.77 0.94
rs27071
T
C
0.35 0.19 0.12 0.26
5
1 347 239
0.77 0.94
rs27068
C
T
0.34 0.19 0.12 0.27
5
1 356 684
rs37004
C
T
0.02 0.14 0.12 0.24
Melano
H1
NRSF,STAT
Nr2f2
7 altered motifs
10 cell
types
Th1,8988
T,Hepatoc
ytes
8 cell types
13 bound
proteins
ReguomeDB4
RefSeq genes
2.9kb 3' of
MIR4457
871bp 3' of
MIR4457
2.8kb 5' of
MIR4457
3.7kb 5' of
MIR4457
517bp 3' of
CLPTM1L
CLPTM1L
6 altered motifs
0.68 0.92 rs36115365
1
Motifs changed
dbSNP
func
annot
Smad,TCF12
1 313 242
1
eQTL
tissues
PanIsletD
LNCaP,Os
teobl
5
rs380145
DNAse5
Medullo,i
PS
14 cell
types
Urothelia
Proteins
bound
GTF2F1,POL2
S2,ZNF263
4 altered motifs
EBF,Sin3Ak-20,Zbtb12
2.2kb 5' of
CLPTM1L
12kb 5' of
CLPTM1L
7
6
5
4
4
5
6
(c) 6p21.33
chr
pos (hg19)
LD LD
(r²)2 (D')2
6
31408329
0.52 0.79
6
31410521
6
6
31414051
31414241
6
6
6
31418810
31427395
31428920
0.53 0.79
variant1
rs3132473
AFR AMR ASN EUR GERP
Ref Alt freq freq freq freq cons3
T
A
CT
TT
0.53 0.79 rs141516569 TT
0.52 0.78 rs9267092 G
0.4 0.8
0.47 0.8
0.56 0.82
rs3093958
rs3131623
rs9267123
rs3130477
T
G
T
A
0.01 0.02
C
T
0.01 0.02 0 0.08
0.03 0.02 0.01 0.09
C
0
0.08
0.04 0.02 0.01 0.09
31430010
0.56 0.82
rs3132089
G
A
0.04 0.02 0.01 0.09
6
31430065
0.56 0.82
rs3099839
C
T
0.04 0.02 0.01 0.09
31430694
0.56 0.82
rs3094605
G
C
HepG2
0.04 0.09 0.02 0.11
0.02 0.02 0.02 0.1
6
6
Enhancer
histone marks
DNAse5
Proteins
bound
40 cell
types
4 bound
proteins
0.02 0.02 0.01 0.09
G
A
C
Promoter
histone
marks
0.04 0.02 0.01 0.09
H1, HepG2
6
31430752
0.56 0.82
rs3132090
G
A
0.02 0.02 0.01 0.09
6
31431813
0.56 0.82
rs3130907
A
G
0.04 0.02 0.01 0.09
H1, HepG2
GM12878,
NHEK
6
31433693
0.56 0.82
rs3128986
T
C
0.04 0.02 0.01 0.09
GM12878
6
31434331
0.56 0.82
rs3131619
A
T
6
31434366
0.56 0.82
rs3094013
G
6
6
31434520
31434621
0.51 0.82
0.59 0.82
rs3094012
rs3131618
6
31436738
6
RefSeq genes
ReguomeDB4
7
20kb 5' of HCP5
4
14 altered motifs
Mef2
17kb 5' of HCP5
17kb 5' of HCP5
6
Monocyte
sCD14+_R
O01746
AP-2,Hltf,Hsf
12kb 5' of HCP5
3.6kb 5' of HCP5
5
7
FibroP,NH
DF-Ad,WI38
4 altered motifs
2kb 5' of HCP5
945bp 5' of
HCP5
890bp 5' of
HCP5
261bp 5' of
HCP5
203bp 5' of
HCP5
5
11 altered motifs
5 cell types
Pou2f2,Smad3
4 cell types
4 cell types
Motifs changed
CAC-bindingprotein,Foxj2
dbSNP
func
annot
23kb 5' of HCP5
GM12878,
NHEK, NHLF
H1
eQTL
tissues
NHEK,Cac
o-2
HepG2
5 bound
proteins
11 bound
proteins
4 altered motifs
8 altered motifs
POL2
RXRA
POL2
9 altered motifs
0.04 0.02 0.01 0.09
POL2
Pax-5
A
0.04 0.02 0.01 0.09
AIRE
G
A
C
G
0.09 0.04 0.01 0.09
0 0.02 0 0.08
POL2
POL2,POL24H
8
POL2
4 altered motifs
CDP
0.67 0.88 rs76650611
A
T
0.1 0.02 0.05 0.08
GM12878
31442782
0.48 0.88
rs3131643
G
A
0.13 0.04 0.05 0.11
HMEC
CTCF
4 altered motifs
6
31448564
0.62 0.88
rs3099843
G
T
0.15 0.04 0.05 0.09
6
31448976
0.62 0.88
rs3099844
C
A
0.15 0.04 0.05 0.09
HepG2
6 altered motifs
6
31449552
0.69 0.86
rs3130908
T
C
0.11 0.02 0.05 0.08
HepG2
11 altered motifs
6
31449710
0.62 0.88
rs3130909
T
C
0.11 0.04 0.06 0.09
HepG2
6 altered motifs
6
31450637
0.62 0.88
rs3131642
G
A
0.14 0.04 0.04 0.09
Osteobl
15 cell
types
4 altered motifs
HCP5
106bp 3' of
HCP5
744bp 3' of
HCP5
779bp 3' of
HCP5
933bp 3' of
HCP5
1kb 3' of HCP5
2.3kb 5' of
HCG26
2.6kb 3' of
HCG26
8.4kb 3' of
HCG26
8.8kb 3' of
HCG26
9.4kb 3' of
HCG26
9.5kb 3' of
HCG26
10kb 3' of
HCG26
6
6
2b
2a
3'-UTR
5
3a
5
5
5
5
4
7
6
6
7
7
chr
pos (hg19)
LD LD
(r²)2 (D')2
6
31451370
0.62 0.88
rs3132470
A
G
0.11 0.04 0.05 0.09
6
31451836
0.62 0.88
rs3094011
T
C
0.15 0.04 0.05 0.09
6
31451848
0.62 0.88
rs3094010
C
T
0.15 0.04 0.05 0.09
variant1
AFR AMR ASN EUR GERP
Ref Alt freq freq freq freq cons3
6
31462135
0.7
0.9
rs3130923
G
A
0.1 0.02 0.05 0.08
6
6
6
6
6
6
6
31465047
31469774
31473746
31473957
31476458
31482097
31483481
0.7
0.7
0.74
0.68
0.75
0.76
0.75
0.9
0.9
0.92
0.92
0.92
0.92
0.92
rs3094005
rs3095233
rs3130616
rs3134900
rs3130614
rs3130612
rs9267445
G
A
G
C
T
T
G
T
G
A
G
A
G
C
0.1
0.1
0.1
0.11
0.03
0.01
0.09
6
31492453
0.46 0.94
rs3093988
G
A
0.09 0.06 0.05 0.13
6
31496569
0.45 0.94
rs2516482
A
6
6
31501558
31505480
0.46 0.94
0.74 0.92
rs1055384
rs2734583
0.03
0.03
0.03
0.04
0.02
0.02
0.03
0.05
0.05
0.05
0.05
0
0
0.05
0.08
0.08
0.08
0.09
0.08
0.08
0.08
A
G
Enhancer
histone marks
DNAse5
HIPEpiC,S
KMC
Proteins
bound
CEBPB
9 cell types
GM12878,
HepG2, H1
6 cell types
GM12878
5 bound
proteins
HMEC
G
A
A
G
0.09 0.06 0.05 0.13
0.09 0.03 0.05 0.08
6
31543031
0.45 0.94
rs1800629
G
A
0.1 0.07 0.06 0.14
6
6
31546850
31558702
0.79 0.94
0.72 0.88
rs1800628
rs3130063
G
C
A
T
0.03 0.02 0 0.08
0.07 0.03 0.04 0.08
6
6
31566168
31582025
0.8 0.96
0.42 1
rs3130631
rs3132451
C
G
G
C
0.07 0.03 0.04 0.08
0.22 0.09 0.06 0.16
6
6
6
6
6
31587083
31589264
31591808
31592524
31592636
0.46
0.46
0.46
0.46
0.46
rs3130621
rs3115665
rs3130070
rs3130622
rs3115664
T
C
A
G
C
C
G
G
C
T
0.22
0.22
0.22
0.22
0.22
6
6
6
31596138
31597700
31597875
1
1
0.43 0.98
0.45 0.98
rs3132450
rs3130623
rs3130624
A
C
A
G
T
G
0.04 0.02 0 0.07
0.24 0.08 0.06 0.15
0.24 0.09 0.06 0.15
6
6
6
31598489
31600820
31600851
0.45 0.98
0.45 0.98
0.45 0.98
rs3130626
rs2736157
rs3130627
A
A
G
G
G
T
0.22 0.08 0.06 0.15
0.22 0.08 0.06 0.15
0.22 0.08 0.06 0.15
0.08
0.09
0.08
0.08
0.08
0.06
0.06
0.06
0.06
0.06
0.15
0.15
0.15
0.15
0.15
7 altered motifs
BRCA1,HNF4
HepG2
LUN-1
POL2,POL24H
8
POL2,POL24H
GM12878
8
KAP1
rs3093975
rs9267488
CEBPA,CEBPB
5 altered motifs
Bbx,Sox
21 altered motifs
ATF3,NRSF
Ets,Mef2
6 altered motifs
HNF4,Rad21
0.09 0.03 0.05 0.08
0.44 0.92
0.74 0.92
Motifs changed
Ets
25 cell
types
Fibrobl,W
ERI-Rb-1
31506138
31514247
eQTL
tissues
Pou3f3
G 0.1 0.07 0.06 0.14
A,G,
C T 0.09 0.06 0.05 0.13
6
6
1
1
1
1
1
Promoter
histone
marks
GM12878
4 cell types
HepG2
HepG2
5 cell types
GM12878,
NHEK, HMEC
NHEK,
GM12878,
HMEC
GM12878
GM12878, K562
HepG2
GM12878, K562
9 cell types
GM12864
POL24H8,POL
2
HepG2
5 bound
proteins
CD20+
POL2
Th1,Chori
on
POL2,POL2B
Chorion
POL24H8
POL24H8
HMEC,CM POL2,POL24H
K
8,POL2B
Osteobl
Osteobl
POL24H8
RefSeq genes
11kb 3' of
HCG26
12kb 3' of
HCG26
12kb 3' of
HCG26
3.7kb 5' of MICB
806bp 5' of
MICB
MICB
MICB
MICB
MICB
3.2kb 3' of MICB
4.6kb 3' of MICB
4.3kb 5' of
MCCD1
168bp 5' of
MCCD1
dbSNP
func
annot
ReguomeDB4
4
7
7
2b
intronic
intronic
missense
intronic
5
7
6
7
6
6
7
7
7
DDX39B
intronic
5
DDX39B
intronic
5
4 altered motifs
DDX39B
ATP6V1G2
intronic
intronic
4
5
ATF3,CCNT2,SP1
317bp 5' of TNF
1f
6 altered motifs
Rad21,SMC3
737bp 3' of TNF
NCR3
intronic
4
5
HIF1,HNF4
7 altered motifs
5.4kb 5' of NCR3
967bp 5' of AIF1
1.4kb 5' of
9 altered motifs
PRRC2A
5 altered motifs
PRRC2A
PRRC2A
ZNF219,Zfp281
PRRC2A
CEBPA,CEBPD,Zbtb3
PRRC2A
Cdx,Pbx3
GATA,HEN1
AP-1,BCL
9 altered motifs
PRRC2A
PRRC2A
PRRC2A
PRRC2A
PRRC2A
PRRC2A
3a
5
intronic
intronic
intronic
intronic
intronic
intronic
intronic
synonym
ous
intronic
intronic
6
2b
6
5
6
4
1f
5
1f
1f
4
chr
6
pos (hg19)
31601843
LD LD
(r²)2 (D')2
0.45 0.98
6
6
31603770
31604591
0.46
0.46
1
1
rs11229
rs10885
6
31606398
0.47
1
rs3130046
6
31606677
0.54
1
6
6
6
31606901
31609272
31610479
0.47 1
0.45 0.98
0.46 1
rs5875328
rs3130628
rs3130047
A
CAA
C AG
T C
C T
6
31619576
0.46
rs3117583
A
1
0.48 0.84
variant1
rs3115663
AFR AMR ASN EUR GERP
Ref Alt freq freq freq freq cons3
T C 0.23 0.08 0.06 0.15
Promoter
histone
marks
Enhancer
histone marks
DNAse5
Fibrobl
Proteins
bound
PanIslets
HL-60
eQTL
tissues
Motifs changed
6 altered motifs
RefSeq genes
PRRC2A
AP-3,En-1,p300
11 altered motifs
dbSNP
func
annot ReguomeDB4
intronic
5
synonym
ous
7
missense
1f
A
C
G
T
0.23 0.08 0.06 0.15
0.23 0.08 0.06 0.15
C
AA
AA
rs199920659 AC
G
0.23 0.08 0.06 0.15
Myc,Zfx
PRRC2A
PRRC2A
405bp 3' of
BAG6
0.22 0.08 0.06 0.13
18 altered motifs
126bp 3' of
BAG6
CDP
HEN1
PU.1,RXRA,STAT
BAG6
BAG6
BAG6
3'-UTR
intronic
intronic
4
1f
5
5 altered motifs
BAG6
intronic
1f
11bp 5' of BAG6 intronic
3a
42bp 5' of BAG6 intronic
APOM
intronic
25bp 3' of
ATF3,Hand1,Smad3
APOM
AhR,Pbx3
GPANK1
intronic
2b
7
0.23 0.08 0.06 0.15
0.25 0.09 0.06 0.15
0.23 0.08 0.06 0.15
POL2
HepG2, K562,
Huvec
6 cell types
rs9279379
G 0.23 0.08 0.06 0.15
C,C
CT C 0.11 0.08 0.03 0.1
8 cell types
Huvec
8 cell types
Huvec
HepG2
6
31620489
6
6
31620520
31624864
1
1
1
1
rs3117582
rs3117581
T
A
G
G
0.04 0.02
0.04 0.03
6
6
31626013
31630968
1
0.46
1
1
rs3132449
rs3117580
C
G
T
A
0.04 0.03 0 0.07
0.23 0.08 0.06 0.15
GM12878
NHLF
4 cell types
6 cell types
6
31632134
0.47
1
rs3130618
C
A
0.23 0.08 0.06 0.15
NHLF, H1
6 cell types
6
6
31633496
31636742
0.46
1
1
1
rs3117579
rs9267531
G
A
T
G
0.23 0.09 0.06 0.15
0.04 0.03 0 0.07
9 cell types
6
31666424
0.92 0.96
rs9267539
A
C
0.05 0.03
6
6
31671557
31677391
1
1
1
1
rs9267544
rs9267549
C
G
A
A
0.04 0.02 0 0.07
0.05 0.03 0.01 0.07
7 cell types
6
31704294
0.98
1
rs3131383
G
T
0.06 0.03
0
0.08
9 cell types
6
6
6
6
6
6
31705864
31708463
31709778
31712196
31714031
31715882
0.98
0.98
0.98
0.98
0.98
0.98
1
1
1
1
1
1
rs3101018
rs3131381
rs3131380
rs3132445
rs3132443
rs3130484
C
C
A
G
G
T
T
A
G
A
A
C
0.04
0.06
0.06
0.06
0.05
0.06
0.02
0.03
0.03
0.03
0.02
0.03
0
0
0
0
0
0
0.08
0.08
0.08
0.08
0.08
0.08
H1
7 cell types
6
6
6
6
6
6
6
31718396
31721033
31725230
31725285
31726253
31726794
31727474
0.98
0.98
0.93
0.98
0.98
0.98
0.98
1
1
1
1
1
1
1
rs3117573
rs3131379
rs3117574
rs3131378
rs3117575
rs3117576
rs3117577
C
G
G
A
T
T
A
G
A
A
G
C
C
G
0.05
0.06
0.06
0.06
0.05
0.06
0.04
0.02
0.03
0.03
0.03
0.02
0.03
0.02
0
0
0
0
0
0
0
0.08
0.08
0.08
0.08
0.08
0.08
0.08
0
0
0
0.07
0.07
6 cell
types
112 cell
types
71 cell
types
39 bound
proteins
42 bound
proteins
H9ES,Hep HNF4A,HNF4
atocytes
G,POL2
5 cell
23 bound
types
proteins
0.07
Huvec, K562
K562, HepG2
8 cell types
HepG2, K562
K562
K562
HepG2
HepG2
K562
HSMM, NHLF
POL2
99 cell
types
104 cell
types
21 cell
types
31 bound
proteins
25 bound
proteins
PU1,ZNF263
5 bound
proteins
POL2
7
E2F,Zfp161,Znf143
ATF3,THAP1
5
7
NRSF,TCF12
GPANK1
missense
1f
12 altered motifs
CTCF,Rad21
Hoxa5,NRSF,Sin3Ak20
GPANK1
CSNK2B
5'-UTR
intronic
2b
6
intronic
6
4 altered motifs
ERalpha-a,VDR
ABHD16A
419bp 5' of
ABHD16A
LY6G6F
intronic
5
7
NRSF,Sin3Ak-20
CLIC1
5'-UTR
4
intronic
intronic
intronic
intronic
intronic
4
4
7
5
6
6
intronic
intronic
intronic
intronic
intronic
intronic
intronic
4
1f
7
6
7
7
7
4 altered motifs
1.5kb 5' of CLIC1
11 altered motifs
MSH5
LBP-9,RREB-1,Spz1
MSH5
BCL,NRSF,Sin3Ak-20
MSH5
5 altered motifs
MSH5
MSH5
E2F,Nrf1
TAL1
8 altered motifs
SRF,TATA
RXRA,SETDB1
MSH5
MSH5
MSH5
MSH5
MSH5
MSH5
MSH5
chr
pos (hg19)
LD LD
(r²)2 (D')2
6
31727897
0.98
6
31733466
6
0.98
1
1
variant1
rs3115672
AFR AMR ASN EUR GERP
Ref Alt freq freq freq freq cons3
C
0.06 0.03
0
Enhancer
histone marks
C
0.06 0.03
0
0.08
HepG2
H1
31733950
C
0.06 0.03
0
0.07
6
31734345
0.98
HepG2, H1
H1, HepG2,
HSMM
HMEC
HMEC, NHLF,
Huvec
6
31739120
6
rs3115671
G
T
0.06 0.03
0
0.08
0.94 0.98
rs3130490
G
T
0.06 0.03
0
0.08
K562, NHEK
31745464
0.94 0.98
rs3130491
G
A
0.02
0
0.08
5 cell types
6
31749142
0.94 0.98
rs915652
G
A
0.01 0.02
0
0.08
6
6
6
6
6
6
6
6
6
31749184
31754830
31761213
31765863
31765864
31765984
31766660
31768799
31772093
0.94
0.93
0.86
0.51
0.57
0.87
0.89
0.91
0.91
0.98 rs915651
G
0.98 rs2753961 T
0.96 rs2607014 G
0.92 rs199998896 T
0.96 rs1144710 T
0.96 rs2736425 G
0.96 rs2763980 C
0.96 rs681331
A
0.96 rs625421
C
A
C
A
TA
A
A
T
C
A
0.05
0.05
0.05
0.32
0.22
0.05
0.04
0.05
0.05
6
31777192
0.91 0.96
rs553414
A
G
0.05 0.02
6
31787167
0.89 0.96
rs1265947
C
T
0.06 0.04 0.02 0.08
0
0.02 0 0.08
0.02 0 0.08
0.03 0 0.08
0.09 0.04 0.12
0.08 0.02 0.11
0.02 0 0.08
0.03 0 0.08
0.02 0 0.08
0.02 0 0.08
6
31798134
0.91 0.96 rs144929896 TA
T
0.05 0.02
6
31799076
0.81 0.94
rs3115674
T
G
6
31802101
0.91 0.96
rs3130476
C
6
31805913
0.91 0.96
rs3130478
C
0
0
DNAse5
0.08
0.08
Urothelia,
Caco-2
4 cell
types
28 cell
types
HeLaS3,Fibrobl
,Jurkat
Huh7,MCF7,Urotheli
a
LNCaP,Ca
co-2
LNCaP,Ca
co-2
HMEC
CEBPB
5 cell
types
T
0.05 0.02
0
0.08
7 cell types
K562, Huvec
T
0.01 0.04
0
0.08
6 cell types
HepG2, Huvec
NHEK
0.02
0
0.08
WERI-Rb1
0.05 0.02
0
0.08
HeLa-S3
A,T 0.05 0.02
0
0.08
0
0.07
0.91 0.96
rs3130679
A
G
6
31808436
0.91 0.96
rs599707
C
T
6
31810612
0.91 0.96
rs9267574
C
6
31818108
0.89 0.94
rs9267578
C
T
0.02 0.02
6
31826705
0.58 0.96 rs67682613
G
A
0.18 0.07 0.06 0.11
eQTL
tissues
RefSeq genes
Nr2f2
MSH5
9 altered motifs
C6orf27
missense
5
18 altered motifs
C6orf27
8 altered motifs
C6orf27
intronic
synonym
ous
4
Pbx3,SIX5,TBX5
C6orf27
intronic
5
11 altered motifs
VARS
intronic
2b
12 altered motifs
VARS
intronic
5
8 altered motifs
Pax-5
11 altered motifs
7 altered motifs
9 altered motifs
4 altered motifs
Myc,Pax-4
17 altered motifs
4 altered motifs
VARS
VARS
VARS
LSM2
LSM2
LSM2
LSM2
LSM2
LSM2
202bp 3' of
HSPA1L
1.4kb 3' of
HSPA1A
102bp 3' of
HSPA1B
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
5
7
6
NRSF,SETDB1,Zfx
SIRT6
POL2,CHD2
4 bound
proteins
POL2,POL24H
8
POL2,HEY1
6
7
7
6
6
7
5
TCF12
1kb 3' of
HSPA1B
590bp 5' of
C6orf48
Ets,Pax-4
C6orf48
intronic
5
C6orf48
894bp 3' of
C6orf48
3.1kb 3' of
C6orf48
8.7kb 3' of
NEU1
122bp 3' of
NEU1
3'-UTR
5
15 altered motifs
GZF1
K562
13 altered motifs
CEBPB
dbSNP
func
annot ReguomeDB4
synonym
ous
6
Motifs changed
CACD,NRSF
4 cell types
6 cell types
31807540
CTCF,POL2
K562, HepG2
0.08 0.03 0.02 0.08
6
POL2,TAF1
5 cell types
8 cell types
NHLF,
GM12878,
HMEC
0
Proteins
bound
0.08
T
CA
0.94 0.98 rs150731509 G
1
rs3101017
T
Promoter
histone
marks
AP-1,NF-E2
5
4
5
6
7
5
chr
6
6
6
pos (hg19)
31832038
31835164
31840477
LD
(r²)2
0.91
0.54
0.84
LD
(D')2
0.96
0.94
0.92
variant1
rs515688
rs693906
rs501942
6
31870326
0.85 0.92
rs558702
AFR
Ref Alt freq
A G 0.06
G C 0.18
C T 0.05
G
A
Promoter
AMR ASN EUR GERP histone
freq freq freq cons3
marks
0.03 0 0.08
7 cell types
0.07 0.06 0.11
0.02 0 0.08
0.07 0.02
0
0.07
7 cell types
Enhancer
histone marks
K562, NHEK
HepG2
NHLF, K562
DNAse5
17 cell
types
Proteins
bound
4 bound
proteins
eQTL
tissues
Motifs changed
MAZ,Mef2
5 altered motifs
9 altered motifs
RefSeq genes
SLC44A4
SLC44A4
SLC44A4
dbSNP
func
annot
intronic
intronic
intronic
C2
intronic
ReguomeDB4
6
6
6
3a
(d) 9p21
chr
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
pos (hg19)
22 050 898
22 059 905
22 060 136
22 064 465
22 065 002
22 067 593
22 072 264
22 072 301
22 072 638
22 072 719
22 076 071
22 076 795
22 077 085
22 077 543
22 081 397
22 081 850
22 083 404
22 084 310
22 085 598
22 087 473
22 088 090
22 088 094
22 088 260
22 090 301
22 090 521
22 090 603
22 090 936
22 091 069
22 091 924
22 092 257
22 092 924
22 094 330
22 094 796
22 096 055
LD
(r²)2
0.41
0.48
0.48
0.51
0.49
0.5
0.61
0.62
0.62
0.52
0.59
0.65
0.67
0.56
0.68
0.68
1
0.66
0.66
0.52
0.59
0.59
0.59
0.46
0.43
0.51
0.5
0.5
0.45
0.51
0.55
0.53
0.56
0.57
LD
(D')2
0.81
0.93
0.93
0.94
0.92
0.92
0.92
0.94
0.94
0.94
0.94
0.95
0.97
0.95
0.99
0.99
1
0.99
0.99
0.96
0.92
0.92
0.92
0.89
0.9
0.92
0.94
0.92
0.88
0.89
0.89
0.89
0.89
0.89
AFR
variant1
Ref Alt freq
rs944800
A G 0.99
rs10757268 T C 0.99
rs2095144 A G 0.99
rs8181047 A G 0.99
rs10811647 C G 0.15
rs10811650 A G 0.18
rs10757269 A G 0.91
rs9632884 G C 0.97
rs9632885 G A 0.78
rs10757270 A G 0.34
rs1831733 T C 0.21
rs10757271 A G 0.95
rs10811652 A C 0.97
rs1412832 C T 0.99
rs10116277 G T 0.95
rs6475606 C T 0.95
rs1333040 C T 0.65
rs1537370 C T 0.71
rs1970112 T C 0.53
rs7857345 T C 0.98
rs10738606 A T 0.24
rs10738607 A G 0.24
rs10757272 C T 0.22
rs10757273 C A 0.46
rs9644859 G A 0.47
rs9644860 C T 0.47
rs9644862 T G 0.76
rs10811653 C T 0.47
rs7866503 G T 0.45
rs2210538 G A 0.5
rs141014318 A G 0.18
rs4977757 A G 0.82
rs10738608 A C 0.88
rs10757274 A G 0.21
AMR
freq
0.86
0.86
0.86
0.86
0.42
0.43
0.54
0.54
0.52
0.44
0.46
0.54
0.54
0.86
0.53
0.53
0.57
0.5
0.47
0.87
0.47
0.47
0.47
0.49
0.49
0.5
0.48
0.49
0.47
0.49
0.44
0.5
0.52
0.47
ASN
freq
0.9
0.89
0.89
0.89
0.49
0.49
0.82
0.73
0.52
0.52
0.52
0.82
0.72
0.72
0.7
0.7
0.7
0.7
0.51
0.69
0.69
0.69
0.69
0.67
0.59
0.63
0.6
0.61
0.59
0.7
0.47
0.65
0.67
0.48
EUR GERP
freq cons3
0.68
0.71
0.71
0.7
0.44
0.44
0.49
0.49
0.49
0.44
0.47
0.49
0.49
0.68
0.48
0.48
0.58
0.48
0.48
0.71
0.49
0.49
0.48
0.44
0.42
0.45
0.43
0.44
0.44
0.46
0.48
0.47
0.49
0.49
Promoter
histone
marks
Enhancer
histone marks
4 cell types
TCF4
NHEK, HMEC
5 cell types
4 cell types
HMEC
A
G
0.19 0.47 0.48 0.49
4 cell types
9
9
9
9
9
22 098 619
22 099 568
22 100 176
22 102 165
22 103 183
0.89
0.91
0.91
0.91
0.91
rs2891168
rs1537371
rs1556516
rs7859727
rs1537372
A
C
G
C
G
G
A
C
T
T
0.2
0.95
0.95
0.79
0.11
4 cell types
NHLF, HMEC
NHLF
4 cell types
6 cell types
9
22 103 341 0.59 0.91
rs1537373
T
G
0.95 0.55 0.69 0.49
6 cell types
9
22 103 813 0.58 0.9
rs1333042
A
G
0.95 0.55 0.69 0.49
9
22 105 927 0.56 0.87
rs7859362
T
C
0.95 0.6 0.69 0.5
5 cell types
NHLF,
GM12878,
HMEC
0.49
0.49
0.49
0.49
0.43
HeLa-S3
CEBPB
HSMM
rs4977574
0.48
0.69
0.69
0.68
0.48
RefSeq genes
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
dbSNP
func
annot ReguomeDB4
intronic
7
intronic
7
intronic
6
intronic
7
intronic
5
intronic
7
intronic
6
intronic
7
intronic
5
intronic
7
intronic
6
intronic
7
intronic
6
intronic
7
intronic
7
intronic
7
intronic
7
intronic
7
intronic
7
intronic
6
intronic
5
intronic
7
intronic
4
intronic
7
intronic
5
intronic
7
intronic
6
intronic
7
intronic
7
intronic
7
intronic
6
intronic
7
intronic
7
intronic
7
Ets,GR
CDKN2B-AS1
intronic
2c
AIRE,GLI
8 altered motifs
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
intronic
intronic
intronic
intronic
intronic
4
7
7
6
5
CDKN2B-AS1
intronic
4
CDKN2B-AS1
intronic
4
CDKN2B-AS1
intronic
6
Motifs changed
GATA
Cdx,HNF1,SRF
4 altered motifs
EBF,Pax-5
4 altered motifs
4 altered motifs
CEBPB,Pax-8
4 altered motifs
ERalpha-a,Rad21
8 altered motifs
SETDB1
5 altered motifs
6 altered motifs
Hoxa13,Mrg1::Hoxa9
PRDM1
Th2
22 098 574 0.57 0.89
0.47
0.55
0.55
0.5
0.43
eQTL
tissues
PrEC
9
0.57
0.59
0.59
0.58
0.47
DNAse5
Proteins
bound
HSMMtub
e,LNCaP
HSMMtub
e,LNCaP
Hoxa5
5 altered motifs
5 altered motifs
Nanog,Nrf1,Zbtb3
Zbtb3
4 altered motifs
Mef2,TATA
4 altered motifs
FAC1
AIRE
5 altered motifs
Irf,RXRA
GR
4 altered motifs
Pbx3
AhR::Arnt,Arnt,RREB-1
Fibrobl,He
La-S3,Th2
41 cell
types
13 bound
proteins
5 bound
proteins
4 altered motifs
LD
(r²)2
0.55
0.56
0.56
0.55
LD
chr pos (hg19)
(D')2
variant1
Ref Alt
9 22 106 225
0.87 rs10757275 G A
9 22 106 271
0.87 rs6475609 A G
9 22 106 731
0.87 rs1333043 T A
9 22 110 131
0.86 rs1412834 T C
139 22 111 585 0.53 0.85 rs148322588 A mer
9 22 112 241 0.54 0.85 rs7341786 A C
AFR
freq
0.22
0.95
0.95
0.95
AMR
freq
0.52
0.6
0.6
0.6
ASN
freq
0.47
0.69
0.69
0.69
EUR GERP
freq cons3
0.49
0.5
0.5
0.5
Enhancer
histone marks
HMEC
HMEC
HMEC
DNAse5
Proteins
bound
eQTL
tissues
GATA,PLZF,Spz1
4 altered motifs
Mef2
RefSeq genes
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
dbSNP
func
annot
intronic
intronic
intronic
intronic
VDR
CDKN2B-AS1
CDKN2B-AS1
intronic
intronic
7
4
4 altered motifs
CDKN2B-AS1
intronic
6
5 altered motifs
Smad3,Smad
CDKN2B-AS1
CDKN2B-AS1
intronic
intronic
6
7
YY1
CDKN2B-AS1
CDKN2B-AS1
intronic
intronic
7
5
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
CDKN2B-AS1
255bp 3' of
CDKN2B-AS1
2.7kb 3' of
CDKN2B-AS1
3kb 3' of
CDKN2B-AS1
3kb 3' of
CDKN2B-AS1
3.4kb 3' of
CDKN2B-AS1
3.4kb 3' of
CDKN2B-AS1
3.4kb 3' of
CDKN2B-AS1
3.4kb 3' of
CDKN2B-AS1
3.5kb 3' of
CDKN2B-AS1
3.7kb 3' of
CDKN2B-AS1
4.3kb 3' of
CDKN2B-AS1
4.4kb 3' of
CDKN2B-AS1
intronic
intronic
intronic
intronic
intronic
intronic
intronic
5
7
7
7
6
6
3a
Motifs changed
0.77 0.56 0.69 0.5
0.95 0.59 0.64 0.5
22 114 495 0.54 0.86 rs10738609
22 115 026 0.55 0.86 rs2383206
C
C
C,G,
A T
A G
5 cell types
5 cell types
HMEC, HSMM,
NHLF
HMEC, HSMM,
NHLF
NHLF
0.21 0.52 0.49 0.5
0.43 0.56 0.49 0.5
NHLF
4 cell types
9
9
9
9
9
9
9
22 115 286
22 115 589
22 115 959
22 116 046
22 116 071
22 116 220
22 119 195
rs944797
rs1004638
rs2383207
rs1537374
rs1537375
rs1537376
rs1333045
T
A
A
A
T
T
T
C
T
G
G
C
C
C
0.43
0.95
0.95
0.95
0.73
0.43
0.47
9
22 121 349 0.45 0.75 rs10217586
A
T
0.47 0.55 0.51 0.52
4 altered motifs
9
22 123 766 0.55 0.88 rs10738610
A
C
0.21 0.52 0.51 0.49
4 altered motifs
9
22 124 123 0.55 0.88
rs1333046
T
A
0.26 0.52 0.51 0.49
7 altered motifs
9
22 124 140 0.56 0.88
rs7857118
A
T
0.95 0.59 0.69 0.5
9
22 112 427 0.54 0.85
rs7341791
A
9
9
22 112 599 0.53 0.85 rs10511701
22 114 469 0.55 0.86 rs10733376
T
G
9
9
0.55
0.55
0.55
0.55
0.54
0.55
0.42
0.86
0.86
0.86
0.86
0.86
0.86
0.74
G
0.93 0.59 0.68 0.5
0.96 0.6 0.69 0.5
Promoter
histone
marks
0.96 0.6 0.69 0.5
0.56
0.6
0.6
0.59
0.56
0.56
0.53
0.48
0.69
0.69
0.69
0.69
0.49
0.51
0.5
0.5
0.5
0.5
0.5
0.5
0.51
HSMM, NHLF
NHLF
NHLF
NHLF
NHLF
NHLF
5 cell types
22 124 450 0.52 0.88 rs10757277
A
G
0.2
0.5 0.51 0.48
HSMM, Huvec
9
22 124 472 0.51 0.88 rs10811656
C
T
0.44 0.53 0.4 0.47
HSMM, Huvec
9
22 124 477 0.52 0.88 rs10757278
A
G
0.2
0.5 0.51 0.48
HSMM, Huvec
9
22 124 504 0.53 0.88
rs1333047
A
T
0.95 0.58 0.69 0.48
9
22 124 630 0.53 0.89 rs10757279
A
G
0.2 0.49 0.51 0.47
HSMM, Huvec
HSMM, Huvec,
HMEC
HSMM, Huvec,
HMEC
22 124 744 0.53 0.88
rs4977575
C
G
0.95 0.57 0.69 0.48
HAc
HA-h,HAsp,HFF
HUVEC
GATA3
TCF12
CCNT2,Evi-1,GATA
Foxl1,Nanog,TATA
4 altered motifs
5 altered motifs
9
9
CFOS
POL2,STAT1,S
HeLa-S3
TAT3
POL2,STAT1,S
HeLa-S3
TAT3
POL2,STAT1,S
HeLa-S3
TAT3
Pax-5,STAT
HeLa-S3
HDAC2,Irf
33 cell
types
STAT1,STAT3
BAF155,STAT
1
9 bound
proteins
Nrf1,STAT
8 altered motifs
9
22 125 347 0.56 0.89
rs1333048
A
C
0.29 0.52 0.51 0.49
DMRT4,DMRT7,Pou1f
1
9
22 125 503 0.54 0.9
rs1333049
G
C
0.24 0.5
HP1-site-factor,RXRA
0.5 0.47
ReguomeDB4
7
6
6
7
7
7
6
6
4
4
4
2a
3a
4
7
7
(e) 12p13.33
LD
(r²)2
0.4
0.63
0.68
LD
(D')2
variant1
Ref Alt
-0.92 rs7953330 G C
0.93 rs7302558 G A
0.96 rs11064598 T A
AFR
freq
0.19
0.33
0.45
AMR
freq
0.27
0.46
0.48
ASN
freq
0.29
0.32
0.32
EUR GERP
freq cons3
0.3
0.44
0.44
chr
12
12
12
pos (hg19)
998819
1044758
1047466
12
1055452
0.69 0.97 rs11064607
A
G
0.45 0.48 0.32 0.44
12
1056454
0.7 0.98 rs59943404
T
G
0.33 0.46 0.32 0.44
12
1058688
1
1
rs3748522
A
C
0.45 0.51 0.32 0.52
Promoter
histone
marks
Enhancer
histone marks
HepG2,
GM12878
NHLF,
GM12878,
HepG2
9 cell types
DNAse5
Proteins
bound
4 cell
types
6 cell
types
12 cell
types
17 bound
proteins
30 bound
proteins
10 bound
proteins
eQTL
tissues
Motifs changed
Hoxa13,Mef2
E2A,TBX5,ZEB1
SIX5,TCF4
RefSeq genes
WNK1
RAD52
RAD52
dbSNP
func
annot
intronic
intronic
intronic
4 altered motifs
RAD52
intronic
5
Zbtb3
RAD52
intronic
7
6 altered motifs
ReguomeDB4
7
7
7
RAD52
intronic
3a
279bp 5' of
12
1059143 0.91 0.98 rs11571379 G A 0.46 0.5 0.32 0.5
7 cell types
NHLF
6 altered motifs
RAD52
2a
417bp 5' of
12
1059281 0.92 1
rs11571378 A T 0.45 0.52 0.32 0.5
7 cell types
NHLF
NF-kappaB,RXRA
RAD52
4
3.6kb 5' of
12
1062430 0.89 0.95 rs10849601 A G 0.45 0.51 0.32 0.51
HepG2
4 cell types
ELF1
RAD52
5
3.6kb 5' of
12
1062479 0.87 0.95 rs10849602 A G 0.45 0.5 0.32 0.51
HepG2
4 cell types
ELF1
20 altered motifs
RAD52
3a
5.6kb 5' of
12
1064438 0.89 0.95 rs10849605 T C 0.45 0.51 0.32 0.51
Osteobl
Pou1f1,TEF-1
RAD52
7
GT
5.8kb 5' of
12
1064628 0.62 0.94 rs138210801 TC G 0.45 0.47 0.31 0.43
7 altered motifs
RAD52
6
TT
5.8kb 5' of
12
1064638
0.4 0.94 rs201176860 C T 0.36 0.37 0.25 0.33
9 altered motifs
RAD52
6
12
1064881 0.61 0.94 rs11064614 G A 0.45 0.47 0.32 0.43
4 altered motifs
6kb 5' of RAD52
7
12
1066834 0.85 0.94 rs55791720 T C 0.34 0.48 0.32 0.51
6 altered motifs
8kb 5' of RAD52
6
8.4kb 5' of
12
1067254 0.59 0.96 rs7955986 C T 0.5 0.6 0.53 0.63
6 altered motifs
RAD52
7
8.9kb 5' of
12
1067758 0.55 0.93 rs4765655 T C 0.56 0.62 0.53 0.63
4 cell types
Osteobl
12 altered motifs
RAD52
6
GM12878,
13 cell
7 bound
9.3kb 5' of
12
1068178 0.59 0.97 rs7300039 A T 0.56 0.62 0.53 0.63
Huvec, HSMM
types
proteins
BCL,Sin3Ak-20,Tgif1
RAD52
4
12
1070308 0.59 0.97 rs10849607 C T 0.55 0.62 0.53 0.63
4 altered motifs
11kb 5' of RAD52
7
12
1072965 0.57 0.97 rs6489769 C T 0.56 0.62 0.53 0.63
Maf,XBP-1
14kb 5' of RAD52
5
Alt, alternative; annot, annotation; Chr, chromosome; Cons, conservation; DNAse HS, DNAse hypersensitivity; Freq, frequency; GERP, Genomic Evolutionary Rate Profiling; LD, linkage disequilibrium; Pos, position, Ref, reference
1 GWAS hits (i.e. replicated SNPs) are emboldened
2 LD (r2) is based upon 1000 Genomes EUR data and a threshold of r2>0.8 was imposed to identify correlated SNPs at all four susceptibility loci
3 GERP scores indicative of evolutionary constraint (>2) are listed
4
RegulomeDB scores: 2b, transcription factor (TF) binding + any motif + DNase Footprint + DNase peak; 3a, TF binding + any motif + DNase peak; 4, TF binding + DNase peak; 5, TF binding or DNase peak; 6, other.
5
Cell types include lymphoblastoid cell lines
SNP positions based on hg19/human