Table S2. SNPs associated with allele-specific expression of Refseq protein coding genes with
published trait- or disease-associations from genome-wide association studies
GWAS genes
CLECL1
IL10
ABO
ABO
TNFSF15
TNFSF15
IL10
RTF1
RNPEP
TP53INP1
TTC39B
ABO
ASE
ASE
p-value
6.18E-95
1.56E-71
2.69E-66
2.69E-66
6.53E-64
6.53E-64
6.34E-62
2.71E-61
6.11E-55
3.92E-53
9.24E-53
5.66E-52
Slope1 LD SNP
-0.32
-0.26
-0.43
-0.43
0.17
-0.17
-0.25
0.11
0.06
0.07
-0.21
0.44
SHBG
ABO
ANGPTL3
SIN3A, PTPN9
ABO
DOCK7
Intergenic
NEGR1
PLEKHH1
TNFRSF10A,
LOC389641
LIPA
PLCL1
NR
TBKBP1
SLC22A4, SLC22A5,
IRF1, IL3
AHI1
ACADS
5.72E-52
1.00E-50
1.04E-50
1.37E-50
3.39E-50
8.78E-49
1.89E-48
1.94E-48
7.92E-48
0.20
0.44
0.09
0.20
0.43
0.09
-0.11
0.27
-0.13
4.87E-47
2.76E-46
1.68E-44
2.44E-44
4.18E-44
-0.07
0.12
0.14
-0.30
0.25
PAX8
DNAH11
SHB
ORMDL3,ZPBP2M,G
SDML
ATF7, ATP5G2
PPM1E
VKORC1
FARP2
ADCY3, DNAJC27
ORMDL3
KCTD7, RABGEF1
HRK, FBXW8
VKORC1
ZBTB38
ZBTB38
3.63E-41 -0.36
6.68E-41 -0.18
9.86E-41 -0.06
LD
rs4950752
1.0
rs1641535
1.0
1.43E-43 -0.10
8.94E-43 -0.22
3.52E-41 -0.07
3.60E-40
1.19E-38
1.86E-38
2.40E-38
3.77E-38
3.99E-38
6.98E-38
1.08E-37
6.88E-37
1.38E-36
2.06E-36
2.06E-36
0.07
-0.11
0.18
0.14
0.05
-0.10
0.07
0.22
-0.15
0.14
0.06
-0.06
rs4849179
1.0
rs6721750
1.0
rs801191
0.889
GWAS
GWAS SNP2 Trait3
rs10466829
rs1518111
rs643434
rs657152
rs4263839
rs6478108
rs1800871
rs2336725
rs4950806
rs896854
rs471364
rs612169
Multiple sclerosis
Behcet's disease
Inflammatory biomarkers
Liver enzyme levels
Crohn's disease
Leprosy
Behcet's disease
Height
Butyrylcholinesterase levels
Type 2 diabetes
HDL cholesterol
Metabolic traits
Sex hormone-binding globulin
rs1641537 levels
rs505922
Protein quantitative trait loci
rs10889353 Triglycerides
rs4886707 Height
rs687621
D-dimer levels
rs1167998 Triglycerides
rs2188962 Crohn's disease
rs2568958 Body mass index
rs1077989 Phospholipid levels (plasma)
Age-related macular
rs13278062 degeneration
rs1412444 Coronary heart disease
rs6738825 Crohn's disease
rs3764021 Type 1 diabetes
rs8070463 Ankylosing spondylitis
rs12521868 Crohn's disease
rs11154801 Multiple sclerosis
rs2066938 Metabolic traits
Renal function-related traits
rs11123170 (BUN)
rs4487645 Multiple myeloma
rs7873102 Brain structure
rs2305480
rs11170631
rs9303401
rs10871454
rs757978
rs6545814
rs2872507
rs10263935
rs7294919
rs9923231
rs6763931
rs724016
Ulcerative colitis
Height
Cognitive test performance
Warfarin maintenance dose
Chronic lymphocytic leukemia
Body mass index
Crohn's disease
Aortic root size
Brain structure
Warfarin maintenance dose
Height
Height
Intergenic
CRCP
Intergenic
MERTK
ZBTB38
IKZF3
MAP2K5, LBXCOR1
PI16
TOB2
SIN3A
KIF11
CHRNB4
ATXN2,PTPN11,SH2
B3
SH2B3, ATXN2
SH2B3
2.34E-36
3.99E-36
4.05E-36
9.37E-36
1.23E-35
1.71E-35
2.03E-34
3.18E-34
3.77E-34
6.63E-34
8.26E-34
3.55E-33
0.06
-0.20
0.20
-0.12
0.06
0.07
-0.05
-0.07
0.06
0.20
0.11
-0.30
PLCE1,NOC3L
MLF1IP
C11orf10
TNFSF15, TNFSF8
GTF2E2
ULK4
ULK4
2.13E-31
2.51E-31
1.11E-30
1.86E-30
8.65E-30
1.30E-29
1.30E-29
NR
NR
1.80E-29 -0.07
2.01E-29 -0.08
HHEX
Intergenic
2.15E-29 0.11
2.43E-29 0.08
OXTR
MS4A
TNFSF8, TNFSF15
CTF1
MS4A4A
FADS1
3.67E-29
4.25E-29
1.57E-28
2.16E-28
2.24E-28
2.98E-28
NR
MAPT
MICA
IL1RL1,IL18R1,IL18R
AP, SLC9A4
3.83E-28 0.08
4.11E-28 0.06
4.23E-28 -0.07
rs4820438
1.0
1.54E-32 0.05
1.54E-32 -0.05
2.69E-32 0.05
0.05
0.06
0.18
0.15
-0.05
-0.05
-0.05
rs4928431
1.0
-0.26
0.06
0.15
0.13
0.06
0.18
rs10476050 0.848
rs2256175
1.0
7.32E-28 0.34
2.39E-27 -0.09
2.73E-27 0.09
2.80E-27 -0.09
5.31E-27 -0.33
6.35E-27 -0.08
9.76E-27 0.05
Coronary heart disease
Aortic root size
Hip geometry
Multiple sclerosis
Height
Primary biliary cirrhosis
Body mass index
Chemerin levels
Vitiligo
Sudden cardiac arrest
Type 2 diabetes
Sudden cardiac arrest
rs10774625 Retinal vascular caliber
rs653178
Celiac disease
rs3184504 Eosinophil counts
Esophageal cancer and gastric
rs3765524 cancer
rs2130392 Kawasaki disease
rs174538
Phospholipid levels (plasma)
rs3810936 Crohn's disease
rs2978263 Cognitive test performance
rs1052501 Multiple myeloma
rs3774372 Blood pressure
Eosinophilic esophagitis
rs9500256 (pediatric)
rs1167796 Systemic lupus erythematosus
Dehydroepiandrosterone
rs2497306 sulphate levels
rs4699052 Testicular germ cell tumor
Depression and alcohol
rs237899
dependence
rs1562990 Alzheimer's disease
rs4246905 Ulcerative colitis
rs11649653 Triglycerides
rs4938933 Alzheimer's disease (late onset)
rs174548
Metabolite levels
Bipolar disorder and
rs11740562 schizophrenia
rs8070723 Parkinson's disease
rs1063635 Rheumatoid arthritis
rs13015714 Celiac disease
Liver enzyme levels (gammars1076540 glutamyl transferase)
MICAL3
1.37E-27 -0.14
IL18RAP,IL12RL2,IL1
8R1,IL1RL1
2.22E-27 0.34
SLC12A7
SLC22A5
RBJ, ADCY3, POMC
IL18RAP, IL18R1,
IL1RL1, IL1RL2
MTCH2
MAN2A2
rs7586970
rs875971
rs6600671
rs17174870
rs6440003
rs907092
rs2241423
rs1405069
rs4822024
rs8028182
rs6583826
rs950776
rs2058660
Crohn's disease
Hematological and biochemical
traits
Asthma
Body mass index
rs10182181 0.924
rs4580814
rs2073643
rs713586
rs1317149
rs871078
rs917997
Celiac disease
rs10838738 Body mass index
rs2677744 Attention deficit hyperactivity
1.0
1.0
disorder
LOC401365,
LOC493754
PLEKHM1, MAPT,
IMP5
CPT1B
ORMDL3
BARD1
CHI3L1
ZFP90
PAFAH1B2
ITIH3, ITIH4
ABO
HLA-A
TNFSF14
HLA-C
LYZ, YEATS4, FRS2
PDE2A, ARAP1
Intergenic
BGLAP,PAQR6,SMG
5,TMEM79,C1orf85,
VHLL,CCT3,C1orf18
2
9.86E-27 -0.20
rs801193
Aortic root size
2.15E-26
2.66E-26
3.09E-26
3.27E-26
3.49E-26
4.93E-26
5.19E-26
7.34E-26
8.83E-26
1.07E-25
1.10E-25
1.35E-25
4.69E-25
5.12E-25
7.15E-25
rs11012
rs5770917
rs7216389
rs6435862
rs4950928
rs6499188
rs7112513
rs2239547
rs579459
rs2517713
rs1077667
rs2395029
rs317689
rs3781913
rs840616
Parkinson's disease
Narcolepsy
Asthma
Neuroblastoma (high-risk)
YKL-40 levels
Ulcerative colitis
Protein quantitative trait loci
Schizophrenia
Soluble E-selectin levels
Nasopharyngeal carcinoma
Multiple sclerosis
Psoriasis
Response to diuretic therapy
Rheumatoid arthritis
Coronary heart disease
0.27
0.17
-0.06
0.07
-0.24
0.06
-0.12
-0.06
0.43
-0.07
0.05
0.12
-0.08
-0.08
-0.05
rs946262
1.0
rs2517722
1.0
ABO
TYW3, CRYZ
HHEX
HHEX
ZBTB38, RASA2
CNNM2
HLA-A
BAT1
ORMDL3
BARD1
CHD1L
C11orf10
FADS2
GSDMB
MS4A6A, MS4A4E
7.93E-25
1.44E-24
1.60E-24
1.60E-24
1.76E-24
2.83E-24
3.64E-24
4.85E-24
9.38E-24
1.35E-23
2.03E-23
2.16E-23
2.16E-23
2.23E-23
2.60E-23
ALPL, NBPF3
3.31E-23 0.28
Intergenic
BIN1
IKZF3,ZPBP2,GSDM
B,ORMDL3
MHC
4.33E-23 0.06
4.69E-23 -0.19
Hematological and biochemical
traits
Angiotensin-converting enzyme
rs495828
activity
rs3931020 Resistin levels
rs1111875 Type 2 diabetes
rs5015480 Type 2 diabetes
rs9857275 Prion diseases
rs7914558 Schizophrenia
rs2860580 Nasopharyngeal carcinoma
rs3853601 Atopic dermatitis
rs2290400 Type 1 diabetes
rs3768716 Neuroblastoma
rs4950322 Protein quantitative trait loci
rs102275
Metabolic syndrome
rs174574
Phospholipid levels (plasma)
rs8067378 Ulcerative colitis
rs610932
Alzheimer's disease
Liver enzyme levels (alkaline
rs1976403 phosphatase)
Electroencephalographic traits in
rs2766692 alcoholism
rs12989701 Alzheimer's disease (late onset)
5.21E-23 0.06
6.16E-23 0.07
rs9303277
rs4313034
LMNB1
CRHR1
AL591893.2
HLA-DRB9, HLADRB5, HLA-DRB1,
HLA-DQA1, HLADQB1, HLA-DQA2
8.26E-23 0.09
9.02E-23 0.28
1.49E-22 0.15
rs959573
rs9303521
rs3124314
Primary biliary cirrhosis
Graves' disease
Parkinson's disease (motor and
cognition)
Bone mineral density (hip)
Hair morphology
rs3129720
Hypothyroidism
7.70E-25 -0.10
-0.43
0.20
0.10
0.10
-0.05
-0.17
-0.07
-0.07
-0.06
0.07
-0.08
-0.17
0.17
-0.06
-0.06
1.63E-22 0.12
rs6684514
rs6767899
0.921
rs3219190
0.889
rs1827293
0.855
rs3135006
1.0
B3GALT4
GNL3, GLT8D1
NISCH, STAB1
MTCH2, NDUFS3,
CUGBP1
FADS2, FADS1, FEN
FADS1, FADS2
FADS1, FADS2,
FADS3
TRIM66
FEN1
CCND3
HLA-B
LOC400680,
ZNF429
PVR
1.85E-22 -0.05
2.24E-22 -0.08
3.92E-22 0.10
rs1799908
1.0
rs2254287
rs11177
rs6784615
LDL cholesterol
Osteoarthritis
Waist-hip ratio
rs4687617
1.0
4.39E-22 -0.07
4.82E-22 -0.16
4.82E-22 0.16
rs7124681
1.0
rs3817334
rs1535
rs174546
Body mass index
Response to statin therapy
LDL cholesterol
rs174547
rs4929923
rs4246215
rs11968166
rs13437082
HDL cholesterol
Menarche (age at onset)
Phospholipid levels (plasma)
Neutrophil count
Height
1.43E-21 -0.09
1.77E-21 0.09
rs2562456
rs7255066
DPYSL5
SH2B3, ATXN2
TNFRSF14, MMEL1
FUT2
2.57E-21
2.58E-21
2.84E-21
2.97E-21
rs1371614
rs11065987
rs3748816
rs492602
FUT2
BOK, THAP4
ATM
2.97E-21 0.06
3.41E-21 0.09
3.59E-21 0.05
rs516246
rs12479254
rs1801516
GP1BA
HHEX
4.40E-21 0.07
4.60E-21 0.10
rs6065
rs7923837
CDK4
SNCA
NUP205
TPM1
PALB2,NDUFAB1,DC
TN5
TRAF3IP2
HS6ST3
PBRM1
APOA1,KIAA0999,L
OC645044
ICOSLG
MAPT
ICOSLG
FUT2
FUT2
FUT2
5.17E-21
7.11E-21
8.86E-21
1.05E-20
-0.10
0.07
0.10
-0.06
rs10876993
rs356220
rs4294134
rs11071720
Pain
Multiple sclerosis
Fasting glucose-related traits
(interaction with BMI)
Hematocrit
Celiac disease
Vitamin B12 levels
Liver enzyme levels (gammaglutamyl transferase)
Brain structure
Melanoma
Hematological and biochemical
traits
Multiple sclerosis
Celiac disease and Rheumatoid
arthritis
Parkinson's disease
Paget's disease
Mean platelet volume
1.63E-20
2.03E-20
2.23E-20
3.34E-20
-0.08
-0.05
-0.13
0.08
rs420259
rs458017
rs2038823
rs2251219
Bipolar disorder
Psoriasis
Diabetic retinopathy
Major mood disorders
3.49E-20
4.83E-20
7.02E-20
8.25E-20
1.49E-19
1.49E-19
1.49E-19
0.11
-0.08
0.05
-0.08
-0.06
0.06
0.06
rs2075292
rs762421
rs12185268
rs2838519
rs503279
rs504963
rs602662
NAPRT1
1.84E-19 -0.12
rs2290416
LOC343052
2.19E-19 0.05
TNFRSF14, MMEL1,
PLCH2, C1orf93
2.45E-19 -0.08
KIAA1598, VAX1
2.91E-19 0.10
rs4434872
Triglycerides
Crohn's disease
Parkinson's disease
Ulcerative colitis
Metabolic traits
Crohn's disease
Folate pathway vitamin levels
Attention deficit hyperactivity
disorder
Conduct disorder (symptom
count)
CFB
rs541862
4.82E-22
4.83E-22
7.69E-22
8.57E-22
1.34E-21
-0.16
-0.08
0.16
0.05
-0.08
0.14
-0.05
0.08
-0.06
3.69E-19 0.06
rs4509157
1.0
rs2000614
1.0
rs7282490
0.962
rs734999
rs7078160
Ulcerative colitis
Orofacial clefts
Age-related macular
degeneration
C11orf9
TNFSF13
GP6
FUT2, RASIP1
ICOSLG
SLC22A4
SLC22A5
KLHDC8B
ACTA2, FAS
HLA-DPA1, HLADPB1, HLA-DPB2
HLA
FCRL3
FCRL3
MMEL1,TNFRSF14
BCO2
CHRNA3, CHRNA5,
PSMA4, LOC123688
CLN8
Intergenic
HLA-DPB1
3.96E-19
4.97E-19
5.21E-19
6.21E-19
8.84E-19
9.67E-19
9.67E-19
1.03E-18
1.22E-18
-0.16
0.19
-0.26
-0.06
-0.08
0.08
0.08
0.14
-0.09
1.38E-18
1.43E-18
1.63E-18
1.63E-18
1.88E-18
2.10E-18
-0.05
-0.08
0.09
-0.09
0.08
0.07
3.39E-18
3.88E-18
4.49E-18
4.85E-18
0.28
-0.05
-0.20
0.06
EREG
ALPL
BET1L
GPLD1
HNRNPC
HLA-DQB2, HLADOB
USP49,MED20,BYSL
,CCND3
LCAT
CHRNA5
CARD9, INPP5E,
SDCCAG3, SEC16A,
SNAPC4
CARD9
CARD9
GFOD2,LCAT
CHRNA3,CHRNA5,C
HRNB4
RASIP1,IZUMO1,FU
T1,FUT2,CA11,FGF2
1,FLJ36070
CD69
C11orf73
GAB2
1.43E-17
1.99E-17
2.15E-17
2.48E-17
3.08E-17
-0.12
-0.25
0.05
-0.11
0.07
HLA-DP, COL11A2
MICA
GDF5, UQCC
NBPF3, ALPL,
RAP1GAP
HBS1L,MYB
FCER1A
1.57E-16 -0.05
1.68E-16 -0.07
2.30E-16 -0.05
rs676388
rs5744256
1.0
1.0
rs174535
rs3803800
rs1671152
rs281379
rs4819388
rs272889
rs274546
rs7617480
rs2234978
Phospholipid levels (plasma)
IgA nephropathy
Platelet aggregation
Crohn's disease
Celiac disease
Metabolic traits
Height
Menarche (age at onset)
Immunoglobulin A
rs1883414
rs2247056
rs3761959
rs7528684
rs3890745
rs1834481
Nephropathy
Triglycerides
Graves' disease
Type 1 diabetes autoantibodies
Rheumatoid arthritis
Interleukin-18 levels
rs8034191
rs11986414
rs11249433
rs9277535
rs10799702 0.821
Lung cancer
Gaucher disease severity
Breast cancer
Hepatitis B
Attention deficit hyperactivity
rs1350666 disorder
rs10799701 Metabolic traits
rs11602954 Mean platelet volume
rs9467160 Liver enzyme levels
rs17197037 Bipolar disorder
3.09E-17 0.17
rs2857151
4.09E-17 -0.07
4.93E-17 -0.07
5.51E-17 -0.27
rs3218097
rs255049
rs2036527
Kawasaki disease
Hematological and biochemical
traits
HDL cholesterol
Pulmonary function
5.77E-17
5.77E-17
5.77E-17
6.13E-17
rs10781499
rs10781500
rs4077515
rs12449157
Ulcerative colitis
Ulcerative colitis
Ulcerative colitis
HDL cholesterol
rs1051730
Nicotine dependence
rs2287921
rs4763879
rs6592284
rs2373115
rs3117242
rs2596542
rs2236164
Retinal vascular caliber
Type 1 diabetes
Cognitive performance
Alzheimer's disease (late onset)
Antineutrophil cytoplasmic
antibody-associated vasculitis
Hepatocellular carcinoma
Height
rs1780324
rs7775698
rs2251746
Liver enzyme levels
Hematology traits
IgE levels
0.05
0.05
0.05
-0.07
6.56E-17 -0.26
7.53E-17
7.89E-17
9.54E-17
1.03E-16
-0.06
0.25
-0.08
-0.07
2.33E-16 0.25
3.02E-16 -0.14
3.74E-16 -0.28
rs973579
0.851
rs7112234
1.0
rs3117213
1.0
rs224415
0.874
CFB,C2
CATSPER4
CRHR1, MAPT
C8orf13, BLK
BLK
NR
CDH1
ALPL
KIAA1271
TIMD4,HAVCR1
LOC100289506
5.35E-16
5.77E-16
5.97E-16
6.33E-16
6.33E-16
7.62E-16
1.10E-15
1.24E-15
1.78E-15
2.17E-15
2.40E-15
-0.06
0.14
-0.28
-0.12
-0.12
-0.09
-0.05
-0.25
0.06
-0.15
-0.10
LOC285830
DUT
2.49E-15 0.06
3.22E-15 -0.36
SLC22A12
FRAP1
MFAP2
NFYC
HLA-DQA2
HAL-DQB2
OPTN
Intergenic
PBX2
ERGIC3
C2orf74,REL
SNCA
3.33E-15
3.53E-15
4.57E-15
8.43E-15
9.50E-15
9.50E-15
1.75E-14
2.62E-14
2.75E-14
3.43E-14
4.17E-14
4.60E-14
HBS1L, MYB
MHC
IL3, ACSL6, P4HA2,
PDLIM4, SLC22A4
4.61E-14 -0.13
5.45E-14 -0.07
TRIM47
PKNOX1
ACE
IRF1
ANGPTL3, DOCK7,
ATG4C
MLN
RFPL1, AP1B1,
THOC5, NF2
SLCO6A1
1.10E-13
1.10E-13
1.15E-13
1.50E-13
FUT2
MAPT
GSDMA
CHRNA5
FBXO40
MHC, C6orf10
BRSK1, TMEM224,
SUV420H2
TF
HBS1L, MYB
2.29E-13
2.36E-13
2.70E-13
2.73E-13
3.33E-13
3.39E-13
0.33
0.09
-0.08
0.06
-0.24
-0.24
-0.15
-0.06
-0.05
-0.06
0.10
-0.06
6.46E-14 -0.06
-0.10
-0.06
0.06
0.07
1.75E-13 -0.07
2.03E-13 0.08
2.09E-13 -0.10
2.28E-13 0.05
-0.05
0.05
-0.05
0.32
-0.05
-0.06
3.63E-13 -0.06
3.72E-13 0.13
4.11E-13 0.13
rs4938493
1.0
rs506338
1.0
rs9435734
1.0
rs3864277
0.961
Age-related macular
degeneration
Height
Head circumference (infant)
Systemic lupus erythematosus
Rheumatoid arthritis
Pain
Colorectal cancer
Folate pathway vitamin levels
Asthma
Cholesterol, total
Multiple sclerosis
Prostate cancer (gene x gene
rs2523395 interaction)
rs11637235 Protein quantitative trait loci
Renal function-related traits
rs504915
(urea)
rs17036350 Corneal curvature
rs2284746 Height
rs4660456 Platelet counts
rs2301271 Systemic lupus erythematosus
rs7453920 Hepatitis B
rs1561570 Paget's disease
rs2302189 Dental caries
rs204993
Asthma
rs2277862 Cholesterol, total
rs10181042 Crohn's disease
rs2736990 Parkinson's disease
Beta thalassemia/hemoglobin E
rs9376092 disease
rs7743761 Ankylosing spondylitis
rs641153
rs11809207
rs11655470
rs13277113
rs2736340
rs17122021
rs9929218
rs4654748
rs4815617
rs6882076
rs758944
rs3091338
rs1055129
rs234720
rs4329
rs2070729
Crohn's disease
White matter hyperintensity
burden
Cognitive test performance
Metabolic traits
Platelet counts
rs12130333 Triglycerides
rs2274459 Obesity (extreme)
Carotid atherosclerosis in HIV
rs13053817 infection
rs1502844 Schizophrenia
Liver enzyme levels (alkaline
rs281377
phosphatase)
rs242557
Progressive supranuclear palsy
rs3894194 Asthma
rs667282
Smoking behavior
rs3772130 Cognitive performance
rs3130340 Bone mineral density (spine)
rs1172822
rs3811647
rs4895441
Menopause (age at onset)
Iron status biomarkers
Mean corpuscular volume
HLA-DRB1
EDC4
SLC28A1, ZNF592,
ALPK3
NR
TACC3,TMEM129,S
LBP,FGFR3
ACSM1
4.48E-13 -0.12
4.59E-13 -0.06
rs9271366
rs8060686
Multiple sclerosis
Coronary heart disease
rs3743162
rs8042374
Alzheimer's disease (age of onset)
Lung cancer
5.54E-13 0.05
6.23E-13 -0.05
rs798766
rs433598
ACE
6.39E-13 -0.06
rs4343
LBH
NTHL1
HLA-DRB1
HLA-DRA
BLK
DDR1, VARS2,
DPCR1
NOTCH4, C6orf10
HLA-A
PSCA
WDR66
NR
Intergenic
C6orf10
SLC22A12
7.21E-13
7.75E-13
8.20E-13
8.20E-13
8.84E-13
0.10
0.06
-0.12
0.12
-0.12
rs7579944
rs2516739
rs3129889
rs3135388
rs1600249
Urinary bladder cancer
Schizophrenia
Angiotensin-converting enzyme
activity
Celiac disease and Rheumatoid
arthritis
Longevity
Multiple sclerosis
Multiple sclerosis
Rheumatoid arthritis
8.84E-13
1.08E-12
1.12E-12
1.22E-12
1.27E-12
1.33E-12
1.40E-12
1.46E-12
1.53E-12
-0.15
0.08
0.06
-0.11
-0.12
0.06
0.05
-0.05
-0.31
rs7756521
rs3130320
rs2523946
rs2294008
rs7961894
rs4380451
rs499818
rs3129943
rs505802
LPL
BCO2
HLA-DRB1
C6orf106
CDKN2A,CDKN2B
LPL
FADS3
BACH2
C20orf132
1.60E-12
1.66E-12
3.01E-12
3.73E-12
3.89E-12
4.05E-12
5.13E-12
5.16E-12
5.35E-12
0.19
-0.05
0.08
0.09
-0.07
0.18
-0.13
-0.07
0.05
DCBLD1
RNF19A, ANKRD46
LPL
PCSK9
C6orf106
ARNT, SETDB1,
LASS2, ANXA9,
MCL1, CTSK
BTNL2
SLC15A2
5.82E-12
5.91E-12
6.04E-12
7.11E-12
7.12E-12
0.10
-0.11
-0.19
0.29
0.09
7.34E-12 -0.06
7.99E-12 -0.08
8.64E-12 0.05
rs7412746
rs3117098
rs4285028
BAIAP2L1
9.04E-12 -0.06
rs9649213
NKAIN3
RP11-24C3.2
LPL
1.09E-11 -0.07
1.10E-11 0.06
1.10E-11 0.18
PCSK7
1.29E-11 -0.13
4.86E-13 -0.05
5.11E-13 0.33
rs12442557 1.0
rs9734313
1.0
rs2043055
0.885
rs17091905
rs2115763
rs3129934
rs2814944
rs1011970
rs10096633
rs174448
rs3757247
rs8115854
rs210648
rs1371867
rs12678919
rs11206510
rs2814993
rs6442117
0.887
rs7834588
rs9876781
rs7841189
rs508487
HIV-1 control
Systemic lupus erythematosus
IgA nephropathy
Bladder cancer
Mean platelet volume
Bipolar disorder
Major CVD
Asthma
Uric acid levels
Cardiovascular disease risk
factors
Interleukin-18 levels
Multiple sclerosis
HDL cholesterol
Breast cancer
Metabolic traits
Phospholipid levels (plasma)
Type 1 diabetes
Hippocampal atrophy
Economic and political
preferences
Atrioventricular conduction
HDL cholesterol
LDL cholesterol
Height
Melanoma
Asthma
Multiple sclerosis
Prostate cancer (gene x gene
interaction)
Response to Vitamin E
supplementation
Longevity
Metabolic syndrome
Cardiovascular disease risk
factors
HLA-C
1.41E-11 0.08
FAM108C1
CDKN2A
RPN2
MHC
IL18R1
FUT8
BIK
CYP4F8
BACH2
1.49E-11
1.66E-11
1.80E-11
1.99E-11
2.48E-11
2.95E-11
2.99E-11
3.14E-11
3.24E-11
TSEN2
Intergenic
3.39E-11 -0.06
5.53E-11 -0.06
rs6766510
rs9917256
PRKAR2B
5.68E-11 -0.11
rs7798500
C6orf10
FAM167A, BLK
BLK
EPS15L1
8.64E-11
9.12E-11
9.12E-11
9.62E-11
rs2050190
rs2254546
rs7812879
rs10411936
WDR12
GNL3
9.73E-11 0.10
1.07E-10 0.06
MHC, other genes
TAS2R38
1.07E-10 -0.05
1.09E-10 0.21
CYP2C18
SHBG
MPDU1
INTS12, NPNT,
FLJ20184, GSTCD
CD40
CD40
CD40
ATP13A2, SDHB
UBXD2
GNL3
GSTCD
MHC
GSDMA
CHRNA3
1.65E-10 -0.05
1.67E-10 0.05
1.67E-10 -0.05
1.68E-10
1.93E-10
1.93E-10
1.93E-10
1.98E-10
2.06E-10
2.71E-10
2.87E-10
3.26E-10
4.32E-10
4.95E-10
0.06
0.09
-0.09
0.09
0.07
0.09
-0.06
-0.06
0.16
-0.05
-0.20
ALDH5A1, GPLD1
FGB, FGA, FGG
ETS1
HLA-DQA2
HSP90B1
C5orf30
HBS1L, MYB
SLC4A7
HLA-C
IL1RL1
NR
5.59E-10
5.68E-10
5.78E-10
6.12E-10
7.30E-10
7.52E-10
8.12E-10
9.67E-10
9.96E-10
1.17E-09
1.26E-09
0.08
-0.05
-0.06
0.14
-0.10
0.10
0.12
-0.09
-0.06
-0.11
-0.08
0.08
-0.07
0.05
0.07
0.19
0.06
0.05
-0.16
-0.07
-0.05
0.10
0.10
-0.06
rs2524069
1.0
rs2811708
0.899
rs1063355
1.0
rs7256818
1.0
rs3134792
rs12148329
rs3731211
rs6031882
rs9272346
rs3771166
rs10483776
rs742134
rs3764563
rs1847472
rs6725887
rs1108842
rs4726481
0.959
rs886424
rs713598
rs12772169
rs12150660
rs4227
rs10050159 1.0
rs2871776
0.883
rs3873379
rs12905
0.851
0.91
rs11727189
rs1569723
rs4810485
rs6074022
rs3738814
rs6430585
rs2590838
rs10516526
rs2269426
rs3859192
rs12914385
Psoriasis
Immune response to smallpox
vaccine (IL-6)
Platelet counts
Hippocampal atrophy
Type 1 diabetes
Asthma
N-glycan levels
Prostate cancer
Inflammatory biomarkers
Crohn's disease
Prostate cancer (gene x gene
interaction)
Parkinson's disease
Adverse response to lamotrigine
and phenytoin
Activated partial thromboplastin
time
Kawasaki disease
Systemic lupus erythematosus
Multiple sclerosis
Myocardial infarction (early
onset)
Adiponectin levels
Bipolar disorder and
schizophrenia
Bitter taste response
Acenocoumarol maintenance
dosage
Testosterone levels
IgA nephropathy
Pulmonary function
Kawasaki disease
Rheumatoid arthritis
Multiple sclerosis
Height
Corneal structure
Adiponectin levels
Pulmonary function
Eosinophil counts
White blood cell count
Pulmonary function
Liver enzyme levels (alkaline
rs1883415 phosphatase)
rs6056
Fibrinogen
rs11221332 Celiac disease
rs2858331 IgE levels
rs1165669 Coronary heart disease
rs26232
Rheumatoid arthritis
rs9494145 Red blood cell traits
rs4973768 Breast cancer
rs9461688 Protein quantitative trait loci
rs1420101 Eosinophil counts
rs4799088 Amyotrophic lateral sclerosis
STARD13
1.27E-09 -0.06
LOC654254
BACH2, MAP3K7
POL3S
HCG27, HLA-C
KIAA1598
HERV, FRD
RORA
AL450992.4
BACH2, MAP3K7
ACAN
Intergenic
PARK16, NUCKS1
C5orf56
NR
ZNF292
CCHCR1
KIF16B
ALPL,NBPF3
SDAD1
SLC14A1
1.31E-09
1.34E-09
1.60E-09
1.70E-09
1.71E-09
1.78E-09
1.96E-09
2.05E-09
2.16E-09
2.87E-09
3.02E-09
3.38E-09
3.83E-09
4.51E-09
4.53E-09
4.55E-09
4.72E-09
5.30E-09
5.91E-09
5.93E-09
0.14
-0.06
-0.07
-0.05
-0.06
0.35
0.12
0.17
-0.07
0.15
0.07
0.15
0.05
0.21
-0.05
0.05
-0.10
-0.19
-0.07
-0.14
TMEM110
HLA
HLA class III
OSBPL7
6.94E-09
6.97E-09
8.17E-09
8.93E-09
-0.10
0.05
-0.15
0.10
HCP5
SYCP2L
SYCP2L
ZNRD1, RNF39
LCAT
AXIN1
HLA-DQB1
HLA-DRA
9.34E-09
9.83E-09
9.83E-09
1.04E-08
1.05E-08
1.06E-08
1.11E-08
1.14E-08
0.06
0.34
-0.34
-0.06
0.06
0.06
0.23
-0.08
MYH15
NR
MC1R
IRF6
CRLF3, ATAD5,
CENTA2, RNF135
1.17E-08
1.21E-08
1.23E-08
1.24E-08
-0.09
-0.06
-0.06
0.13
1.28E-08 0.06
rs3760318
MHC, other genes
GNAT2, GNAI3,
AMPD2
ELOVL2
PMS1
LCAT
TRIM2
Unknown
IHH, CRYBA2, FEV,
SLC23A3, TUBA1
1.29E-08 -0.05
rs2524005
Height
Bipolar disorder and
schizophrenia
rs6537837
rs3734398
rs5743030
rs2271293
rs12644284
rs3764147
Major depressive disorder
Phospholipid levels (plasma)
Subcutaneous adipose tissue
HDL cholesterol
Multiple sclerosis
Crohn's disease
rs1052483
Height
1.34E-08
1.37E-08
1.87E-08
1.90E-08
2.40E-08
2.56E-08
-0.19
-0.34
0.07
0.06
-0.06
0.12
2.65E-08 0.06
rs602133
0.813
rs2894181
0.852
rs370228
0.906
rs6826085
1.0
rs7214410
0.816
rs8523
rs2295600
rs3132685
0.921
1.0
1.0
rs861020
rs2304355
1.0
0.913
rs9315204
rs11723261
rs10806425
rs11865038
rs3869109
rs740363
rs4711171
rs12591650
rs10788819
rs370409
rs2351491
rs11026412
rs823128
rs11745587
rs9469220
rs1925690
rs130067
rs6044003
rs1697421
rs2273
rs7238033
rs3796352
rs9468925
rs185819
rs7206971
rs9469003
rs4713103
rs6918936
rs8321
rs16942887
rs9921222
rs2856718
rs6903608
rs2603127
rs16966142
rs258322
rs642961
Intracranial aneurysm
Immune response to smallpox
vaccine (IL-6)
Celiac disease
Parkinson's disease
Coronary heart disease
Heart failure
Phospholipid levels (plasma)
Subcutaneous adipose tissue
Hair morphology
Graves' disease
Height
Parkinson's disease
Parkinson's disease
Asthma
Crohn's disease
MRI atrophy measures
Prostate cancer
Intelligence
Phosphorus levels
Longevity
Bladder cancer
Immune reponse to smallpox
(secreted IL-2)
Vitiligo
Height
Cholesterol, total
Stevens-Johnson syndrome and
toxic epidermal necrolysis (SJSTEN)
Phospholipid levels (plasma)
Phospholipid levels (plasma)
AIDS progression
HDL cholesterol
Bone mineral density
Hepatitis B
Hodgkin's lymphoma
Hemostatic factors and
hematological phenotypes
Caffeine consumption
Black vs. red hair color
Orofacial clefts
NR
UBE2D1
2.83E-08 0.07
2.91E-08 -0.06
LPL
3.17E-08 -0.11
Intergenic
MRAS
PRKCZ
MRAS
FXR2, SHBG, SAT2,
ATP1B2
3.56E-08
3.79E-08
3.79E-08
3.79E-08
PTGFRN
HLA-A
ATM, C111orf65
PLCL1
STBD1
4.07E-08
4.19E-08
4.52E-08
4.81E-08
5.37E-08
LPL
5.40E-08 -0.10
LPL
LMAN1L, EDC3,
CYP1A2, CYP1A1,
CSK
5.40E-08 0.10
rs9378249 Bipolar disorder
rs16912145 Brain imaging
Metabolic syndrome (bivariate
rs301
traits)
Response to antipsychotic
rs12526186 treatment
rs2306374 Coronary heart disease
rs3753242 Reasoning
rs9818870 Coronary heart disease
Sex hormone-binding globulin
rs727428
levels
Erectile dysfunction and prostate
rs2806864 cancer treatment
rs2571391 IgE levels
rs11212617 Response to metformin
rs7595412 Hip bone size
rs6812193 Parkinson's disease
HDL Cholesterol - Triglycerides
rs13702
(HDLC-TG)
Triglycerides-Blood Pressure (TGrs15285
BP)
5.41E-08 0.05
rs2470893
LAMC2
BTNL2
-0.16
0.06
0.16
-0.06
rs3763288
0.879
rs12660883 1.0
3.86E-08 0.09
-0.09
0.05
-0.05
-0.11
0.12
rs7365057
rs2735097
1.0
1.0
23231 5.46E-08 -0.10
5.56E-08 0.16
5.57E-08 0.06
PLA2G7
HLA-DQB1
HLA-DQA1, HLADQA2
CPEB1
Intergenic
HLA-DQA2
SLC45A3, NUKS1
FADS3
c6orf10, BTNL2,
HLA-DQB1
CCR6
CCR6
NR
HLA-DQA2
ADAMTS10,
MYO1F, PRAM1,
OR2Z1
RBP4
SLA
BACH2
MYCBPAP
SLC22A18
BTN1A1
NR
rs1805017
rs7775228
Caffeine consumption
Non-alcoholic fatty liver disease
histology (other)
Systemic lupus erythematosus
Waist-hip ratio
Lipoprotein-associated
phospholipase A2 activity and
mass
Asthma
rs2647012
rs783540
rs9262632
rs9275572
rs12748961
rs1000778
Systemic lupus erythematosus
Chronic lymphocytic leukemia
HIV-1 control
Alopecia areata
White blood cell types
Sphingolipid levels
rs959903
rs525410
rs2076529
5.58E-08 0.07
5.62E-08 0.11
7.27E-08
7.62E-08
7.78E-08
8.10E-08
9.04E-08
1.14E-07
0.06
-0.23
0.05
0.06
0.08
0.13
1.14E-07
1.17E-07
1.17E-07
1.24E-07
1.27E-07
-0.24
0.10
0.10
0.06
0.20
rs9357152
rs3093023
rs3093024
rs2326679
rs3916765
Primary biliary cirrhosis
Rheumatoid arthritis
Rheumatoid arthritis
Menopause (age at onset)
Type 2 diabetes
1.31E-07
1.39E-07
1.41E-07
1.42E-07
1.46E-07
1.49E-07
1.56E-07
1.56E-07
-0.05
-0.07
0.10
0.06
0.23
0.08
0.10
-0.10
rs7249094
rs10882272
rs853308
rs12212193
rs6504663
rs16928809
rs13194984
rs712039
Height
Retinol levels
Vitiligo
Multiple sclerosis
Visceral fat
Bilirubin levels
Iron status biomarkers
Tuberculosis
rs8043401
0.918
rs3805
1.0
rs11869714 1.0
NOG, DGKE,
TRIM25, COIL, RISK
1.65E-07 -0.06
DLG5
1.81E-07 0.06
ENSG00000173957,
UBXD4, FKBP1B,
FLJ21945
1.81E-07 0.07
PADI4, PADI6,RCC2,
ARHGEF10L
1.86E-07 -0.19
rs4794665
rs10430531 0.915
rs754466
Height
Liver enzyme levels (gammaglutamyl transferase)
rs7561273
Quantitative traits
rs7538876
Basal cell carcinoma
Drug-induced liver injury
(amoxicillin-clavulanate)
Obesity
HLA-A
BDNF
HLA-DRB1, HLADQA1, HLA-DQB1
1.97E-07 -0.05
2.13E-07 -0.07
GCM2, SYCP2L
HLA-DRA
BOLL, PLCL1
CBX1
TNFSF4
2.51E-07
3.03E-07
3.18E-07
3.20E-07
3.34E-07
LPL
IRF4
NR
3.36E-07 -0.10
3.77E-07 0.06
4.30E-07 0.05
rs2083637
rs1033180
rs8014204
WDR92
Intergenic
4.33E-07 0.13
4.52E-07 0.06
rs4078978
rs3115573
SYNRG
PARK16, SLC45A3,
NUCKS1, RAB7L1,
SLC41A1, PM20D1
6.21E-07 -0.10
rs2074409
6.32E-07 -0.21
rs947211
C2,CFB
PUS10
METTL1, CYP27B1
NR
CYP1A1, CYP1A2
6.63E-07
6.83E-07
6.97E-07
7.43E-07
8.82E-07
1
rs10734394 1.0
2.13E-07 -0.06
0.40
-0.14
-0.07
0.08
0.06
-0.07
-0.07
0.12
0.07
0.05
rs2523822
rs988712
rs9275596
rs9268832
0.961
rs2153157
rs7192
rs700651
rs3764400
rs2205960
Nephropathy
Menarche and menopause (age
at onset)
Non-obstructive azoospermia
Intracranial aneurysm
Body mass index
Systemic lupus erythematosus
Waist circumference and related
phenotypes
Celiac disease
Caffeine consumption
Immune reponse to smallpox
(secreted IFN-alpha)
Nephropathy
Response to angiotensin II
receptor blocker therapy
Parkinson's disease
Age-related macular
rs429608
degeneration
rs10188217 Crohn's disease and celiac disease
rs703842
Multiple sclerosis
rs1927702 Body mass index
rs2472297 Coffee consumption
Slope is given in absolute numbers
Listed are all cis-rSNPs associated to a protein coding gene that are also found or are in LD to a SNP
in the GWAS catalog
3
The trait is taken from the GWAS catalog.
2