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. 2015 Aug 5;24(5):748–755. doi: 10.1038/ejhg.2015.172

Table 1. IFN-γ pathway gene variant associations.

Genes CHR SNP AA MAF OR 95% CI P-values
JAK1 1 rs12129819:C>T NC_000001.11:g.64837976C>T (p.(=)) 0.03 1.17 0.91–1.51 0.22
  1 rs310243:G>A   0.35 1.04 0.94–1.15 0.45
  1 rs2274943:G>A   0.06 0.84 0.69–1.02 0.08
  1 rs310244:G>A   0.17 1.13 1–1.27 0.06
  1 rs310247:A>G   0.08 0.98 0.83–1.16 0.85
  1 rs76865550:T>C   0.10 0.96 0.83–1.12 0.63
  1 rs2230588:C>T NC_000001.11:g.64844806C>T (p.(=)) 0.30 1.00 0.9–1.1 0.96
  1 rs2230587:G>A NC_000001.11:g.64845579G>A (p.(=)) 0.22 0.99 0.88–1.1 0.78
  1 rs17127063:G>A NC_000001.11:g.64846659G>A (p.(=)) 0.12 1.10 0.96–1.27 0.17
  1 rs310228:C>A   0.24 1.01 0.9–1.13 0.91
  1 rs310227:T>C   0.35 1.01 0.91–1.11 0.90
  1 rs310224:T>C   0.34 1.01 0.92–1.12 0.77
  1 rs2256298:A>G   0.35 1.00 0.91–1.09 0.92
  1 rs7524842:T>C   0.12 0.87 0.76–1.01 0.06
  1 rs45598436:G>A NC_000001.11:g.64869379G>A (p.(=)) 0.04 1.13 0.89–1.44 0.32
  1 rs310235:G>A   0.49 0.93 0.85–1.02 0.10
  1 rs59600958:G>A   0.10 0.95 0.82–1.1 0.50
  1 rs7548407:T>A   0.17 1.09 0.97–1.23 0.14
  1 rs3806277:C>T   0.05 0.80 0.65–1 0.05
IL23R 1 rs11465757:T>C   0.06 1.06 0.88–1.29 0.55
  1 rs11465759:T>G   0.10 1.02 0.88–1.19 0.76
  1 rs1884444:T>G NC_000001.11:g.67168129T>G p.(H3Q) 0.48 1.00 0.91–1.1 1.00
  1 rs10889665:A>G   0.32 0.93 0.85–1.03 0.19
  1 rs17129690:C>T   0.11 0.95 0.82–1.1 0.46
  1 rs2064689:G>A   0.16 1.12 0.99–1.27 0.07
  1 rs1321157:A>G   0.39 0.98 0.89–1.08 0.67
  1 rs10489630:A>C   0.33 1.04 0.95–1.15 0.38
  1 rs1569922:C>T   0.29 1.07 0.97–1.18 0.20
  1 rs6588250:G>T   0.12 1.06 0.92–1.22 0.45
  1 rs790634:T>C   0.20 1.01 0.9–1.13 0.91
  1 rs7530511:C>T NC_000001.11:g.67219704C>T p.(P310L) 0.28 0.97 0.88–1.08 0.58
  1 rs4655692:G>A   0.32 0.98 0.89–1.08 0.70
  1 rs7523955:C>G   0.46 0.95 0.86–1.05 0.29
  1 rs2201841:A>G   0.13 0.94 0.82–1.08 0.40
  1 rs11209026:G>A NC_000001.11:g.67240275G>A p.(R381Q) 0.001 1.82 0.4–8.27 0.44
  1 rs1343151:A>G   0.25 0.95 0.86–1.06 0.37
  1 rs1008193:C>G   0.12 1.12 0.97–1.29 0.12
IL12RB2 1 rs10889680:T>A   0.39 0.97 0.88–1.07 0.55
  1 rs12131065:A>G   0.28 1.02 0.92–1.14 0.65
  1 rs10489627:G>A   0.31 0.98 0.88–1.08 0.63
  1 rs2066446:A>G   0.20 1.02 0.91–1.15 0.71
  1 rs2066445:C>T   0.35 1.02 0.93–1.13 0.66
  1 rs139325533:T>G   0.01 0.95 0.59–1.53 0.83
  1 rs149711274:T>C NC_000001.11:g.67320393T>C p.(S9P) 0.01 0.88 0.52–1.49 0.63
  1 rs2307147:T>C NC_000001.11:g.67321603T>C (p.(=)) 0.25 0.94 0.85–1.04 0.24
  1 rs146243804:T>C NC_000001.11:g.67321744T>C (p.(=)) 0.002 1.49 0.47–4.74 0.50
  1 rs10489626:G>C   0.22 1.06 0.95–1.18 0.32
  1 rs2307146:A>G NC_000001.11:g.67328273A>G p.(I185V) 0.01 0.88 0.55–1.41 0.59
  1 rs3790562:A>G   0.27 1.02 0.91–1.13 0.77
  1 rs61731150:C>T NC_000001.11:g.67351018C>T p.(A396V) 0.03 0.89 0.64–1.24 0.49
  1 rs2307145:G>C NC_000001.11:g.67367844G>C p.(Q426H) 0.08 0.96 0.81–1.14 0.68
  1 rs6588259:A>T   0.44 1.00 0.89–1.14 0.95
  1 rs142591070:A>-   0.03 0.99 0.74–1.32 0.94
  1 rs2228420:G>A NC_000001.11:g.67386652G>A (p.(=)) 0.14 0.99 0.87–1.12 0.86
  1 rs113226384:G>T NC_000001.11:g.67395587G>T p.(W696L) 0.002 0.36 0.12–1.12 0.08
  1 rs72932861:C>T   0.03 1.11 0.85–1.44 0.44
STAT1 2 rs12468579:G>A   0.50 0.92 0.84–1.01 0.08
  2 rs12693589:T>C   0.19 0.96 0.85–1.09 0.55
  2 rs1400657:T>G   0.26 1.03 0.92–1.15 0.61
  2 rs148970951:TTCT>-   0.03 1.14 0.87–1.5 0.34
  2 rs41363648:T>C   0.06 1.21 1–1.46 0.05
  2 rs3771300:T>G   0.37 0.96 0.87–1.06 0.43
  2 rs16824035:C>T   0.24 1.19 1.06–1.32 0.002
  2 rs13395505:G>A   0.46 1.06 0.96–1.18 0.23
  2 rs35364817:A>C NC_000001.11:g.191839658A>C (p.(=)) 0.02 0.83 0.6–1.15 0.27
  2 rs2066804:G>A   0.14 0.94 0.83–1.08 0.38
  2 rs2280235:A>G   0.16 0.92 0.81–1.05 0.20
  2 rs16833146:T>C   0.28 1.04 0.93–1.16 0.47
  2 rs2280233:T>C   0.17 0.91 0.8–1.02 0.11
  2 rs2066795:G>A   0.38 1.04 0.95–1.15 0.36
  2 rs4853536:G>C   0.10 1.21 1.03–1.42 0.02
  2 rs11887698:G>A   0.42 0.92 0.83–1.02 0.10
  2 rs7562024:T>C   0.47 0.87 0.79–0.96 0.004
  2 rs12693590:A>C   0.13 1.02 0.88–1.18 0.76
  2 rs2066801:G>T   0.06 1.08 0.89–1.31 0.43
  2 rs10173099:C>T   0.004 0.91 0.44–1.87 0.80
  2 rs2066802:A>G NC_000001.11:g.191874667A>G (p.(=)) 0.09 0.93 0.79–1.09 0.36
  2 rs16833172:G>A   0.17 0.96 0.85–1.1 0.58
  2 rs3215260:C>-   0.09 1.00 0.85–1.17 0.96
  2 rs6745710:C>G   0.43 0.98 0.89–1.08 0.75
  2 rs11689880:T>G   0.19 0.99 0.88–1.11 0.87
  2 rs1467199:C>G   0.35 0.98 0.88–1.08 0.62
  2 rs6740131:A>G   0.24 1.01 0.9–1.13 0.89
STAT4 2 rs3024894:G>A   0.17 1.01 0.9–1.15 0.83
  2 rs16833197:C>G   0.11 0.92 0.79–1.07 0.26
  2 rs16833214:A>G   0.27 1.01 0.91–1.13 0.82
  2 rs16833215:A>G   0.41 1.08 0.98–1.19 0.10
  2 rs1400655:G>C   0.30 1.02 0.92–1.13 0.70
  2 rs11686127:C>T   0.10 1.01 0.86–1.18 0.93
  2 rs3024866:G>A   0.10 0.92 0.79–1.08 0.30
  2 rs7601754:G>A   0.14 1.07 0.92–1.23 0.37
  2 rs12990918:C>T   0.41 0.97 0.88–1.08 0.61
  2 rs6434435:G>A   0.26 0.96 0.86–1.07 0.45
  2 rs12463658:C>A   0.12 0.87 0.75–1.01 0.07
  2 rs7582694:G>C   0.19 1.09 0.97–1.23 0.14
  2 rs16833260:C>G   0.28 1.06 0.95–1.18 0.28
  2 rs10174238:A>G   0.43 1.03 0.9–1.17 0.67
  2 rs6752770:A>G   0.34 0.99 0.89–1.1 0.88
  2 rs10201160:A>T   0.19 0.95 0.84–1.07 0.38
  2 rs4853543:A>G   0.29 1.05 0.94–1.17 0.36
  2 rs10931483:A>G   0.46 1.09 0.98–1.2 0.12
  2 rs2356350:A>G   0.33 0.91 0.83–1.01 0.08
  2 rs10189819:T>C   0.36 0.98 0.88–1.09 0.69
  2 rs12991409:T>C   0.07 1.09 0.9–1.31 0.36
  2 rs12327969:G>C   0.48 0.97 0.88–1.07 0.56
  2 rs897200:T>C   0.23 1.00 0.89–1.12 0.99
IL12A 3 rs2243113:A>G   0.15 0.90 0.79–1.02 0.11
  3 rs2243115:T>G   0.09 1.16 0.99–1.35 0.06
  3 rs144143225:G>A   0.01 1.80 0.93–3.5 0.08
  3 rs2243123:T>C   0.15 1.03 0.9–1.17 0.71
  3 rs2243136:T>C   0.12 1.08 0.94–1.25 0.25
  3 rs35990253:G>A NC_000003.11:g.159713215G>A p.(V211M) 0.03 0.97 0.73–1.28 0.82
  3 rs640039:T>C   0.21 0.96 0.86–1.08 0.52
IL6ST 5 rs1900173:A>T   0.47 0.92 0.83–1.01 0.07
  5 rs10068062:T>C   0.23 1.09 0.98–1.21 0.13
  5 rs73756160:T>C   0.17 0.99 0.88–1.12 0.87
  5 rs3730295:C>T   0.003 0.48 0.2–1.19 0.11
  5 rs2228046:T>C NC_000005.10:g.55954899T>C p.(I454T) 0.36 1.08 0.98–1.19 0.12
  5 rs2228043:C>G NC_000005.10:g.55956103C>G p.(L397V) 0.38 1.08 0.97–1.19 0.15
  5 rs3730292:C>T NC_000005.10:g.55963493C>T (p.(=)) 0.12 1.08 0.94–1.25 0.26
  5 rs11742271:A>G   0.17 1.04 0.92–1.17 0.57
  5 rs2228045:T>C NC_000005.10:g.55968314T>C (p.(=)) 0.14 1.17 1.03–1.34 0.02
  5 rs2228044:C>G NC_000005.10:g.55968325C>G p.(R148G) 0.47 0.91 0.83–0.99 0.03
  5 rs3729959:A>G   0.12 0.99 0.86–1.14 0.89
  5 rs142583572:C>T NC_000005.10:g.55969637C>T p.(A95T) 0.003 1.77 0.71–4.39 0.22
  5 rs16884696:T>C   0.13 1.04 0.9–1.2 0.57
IRF1 5 rs17848428:G>A   0.07 0.94 0.79–1.11 0.46
  5 rs9282761:T>C   0.47 1.06 0.97–1.16 0.20
  5 rs960757:G>A   0.001 0.57 0.14–2.42 0.45
  5 rs2549007:T>C   0.45 0.97 0.88–1.06 0.46
  5 rs2549005:C>T   0.45 1.03 0.94–1.14 0.48
IL12B 5 rs3212227:T>G   0.35 0.97 0.88–1.06 0.48
  5 rs149027358:G>A NC_000005.10:g.159320334G>A (p.(=)) 0.01 0.76 0.4–1.44 0.40
  5 rs3213099:G>C   0.09 1.18 1.01–1.39 0.04
  5 rs919766:A>C   0.26 1.04 0.94–1.16 0.44
  5 rs2288831:T>C   0.36 0.96 0.87–1.06 0.40
  5 rs2546893:G>A   0.25 1.12 1.01–1.25 0.04
  5 rs17860508:GC>CTCTAA   0.29 0.94 0.85–1.04 0.22
IFNGR1 6 rs1887415:G>A NC_000006.11:g.137519238A>G p.(P467L) 0.02 1.28 0.93–1.75 0.13
  6 rs11914:A>C NC_000006.11:g.137519588A>C (p.(=)) 0.04 1.05 0.82–1.35 0.68
  6 rs17175350:T>G NC_000006.11:g.137519634T>G p.(H335P) 0.03 0.96 0.74–1.24 0.75
  6 rs7749390:A>G   0.44 0.88 0.8–0.97 0.01
  6 rs2234711:T>G   0.44 0.91 0.83–1 0.05
  6 rs41401746:AA>-   0.08 1.25 1.01–1.56 0.04
  6 rs1327474:T>C   0.03 0.76 0.58–1 0.05
JAK2 9 rs1887427:A>G   0.07 1.03 0.86–1.23 0.76
  9 rs28662982:C>A   0.05 1.07 0.81–1.43 0.63
  9 rs7849191:T>C   0.14 1.07 0.93–1.22 0.36
  9 rs2890618:T>C   0.42 1.03 0.94–1.13 0.53
  9 rs6476934:T>G   0.15 1.00 0.88–1.15 0.95
  9 rs2230722:T>C NC_000009.11:g.5050706T>C (p.(=)) 0.47 1.07 0.98–1.17 0.15
  9 rs151160183:A>C NC_000009.11:g.5078384A>C p.(N691H) 0.001 1.05 0.23–4.75 0.95
  9 rs7048465:A>C   0.32 0.94 0.85–1.03 0.19
  9 rs7857730:T>G   0.06 1.00 0.82–1.21 0.97
  9 rs7870694:C>T   0.25 1.08 0.97–1.2 0.18
  9 rs2104685:T>A   0.15 1.12 0.98–1.28 0.10
  9 rs11793659:A>G   0.16 1.13 1–1.28 0.06
  9 rs62637626:T>A NC_000009.11:g.5126443T>A p.(D1096E) 0.01 0.79 0.5–1.23 0.29
  9 rs12005968:T>G   0.28 1.04 0.93–1.17 0.49
IL23A 12 rs11465744:G>A   0.05 0.78 0.63–0.97 0.02
IFNG 12 rs116364777:G>C   0.02 1.09 0.75–1.58 0.67
  12 rs2430561:T>A   0.20 0.96 0.86–1.08 0.51
  12 rs76012457:C>T NC_000012.11:g.68551993C>T p.(G54D) 0.003 0.63 0.28–1.43 0.27
  12 rs2069705:A>G   0.44 1.01 0.92–1.11 0.84
SOCS1 16 rs33989964:GT>-   0.15 1.01 0.89–1.15 0.83
IL27 16 rs17855750:A>C NC_000016.10:g.28503907A>C p.(S59A) 0.07 1.02 0.85–1.21 0.87
  16 rs147722011:G>T NC_000016.10:g.28502103G>T p.(T112K) 0.01 0.55 0.28–1.11 0.09
  16 rs114571090:G>A   0.02 0.95 0.69–1.31 0.76
TBX21 17 rs111348082:C>T   0.06 0.96 0.8–1.16 0.67
  17 rs138963923:C>T   0.01 1.37 0.89–2.09 0.15
  17 rs11657388:C>G   0.28 1.07 0.97–1.19 0.18
  17 rs11079788:C>T   0.28 1.08 0.97–1.19 0.16
  17 rs16946878:T>C   0.07 0.99 0.83–1.18 0.90
  17 rs12721470:G>A NC_000017.11:g.47745213G>A (p.(=)) 0.07 0.82 0.69–0.99 0.03
  17 rs11657479:T>C   0.13 1.03 0.9–1.17 0.70
  17 rs17244587:G>A   0.06 0.82 0.68–1 0.06
EBI3 19 rs428253:C>G   0.43 0.97 0.88–1.07 0.56
  19 rs78593442:T>C   0.14 0.99 0.87–1.13 0.87
  19 rs10402128:C>G   0.41 0.98 0.9–1.08 0.72
  19 rs4740:A>G NC_000019.10:g.4236999A>G p.(I201V) 0.31 0.94 0.85–1.05 0.31
TYK2 19 rs12720212:T>C   0.02 0.94 0.7–1.28 0.71
  19 rs8108236:G>A   0.12 1.10 0.95–1.26 0.20
  19 rs12720307:C>T   0.11 1.13 0.97–1.31 0.11
  19 rs34046749:G>T NC_000019.10:g.10357771G>T p.(P820H) 0.04 1.00 0.79–1.27 0.98
  19 rs280519:G>A   0.40 0.99 0.9–1.09 0.82
  19 rs2304255:C>T NC_000019.10:g.10364973C>T p.(G363S) 0.07 0.99 0.83–1.18 0.91
  19 rs2304256:C>A NC_000019.10:g.10364976C>A p.(V362F) 0.07 0.99 0.83–1.18 0.92
  19 rs280523:G>A NC_000019.10:g.10366530G>A (p.(=)) 0.18 1.02 0.9–1.15 0.78
  19 rs12720235:A>G   0.17 1.01 0.86–1.18 0.91
  19 rs280501:C>T   0.39 1.01 0.92–1.11 0.86
IL27RA 19 rs35026308:T>C NC_000019.10:g.14042481T>C p.(L188P) 0.02 0.98 0.67–1.43 0.92
  19 rs149346880:C>T NC_000019.10:g.14042755C>T p.(T245M) 0.01 1.23 0.74–2.07 0.43
  19 rs61355201:G>C NC_000019.10:g.14046453G>C p.(V326L) 0.02 1.00 0.73–1.37 0.99
  19 rs143665600:A>G   0.004 1.66 0.79–3.47 0.18
  19 rs76543168:C>T NC_000019.10:g.14050824C>T p.(T490I) 0.05 1.04 0.84–1.28 0.73
  19 rs2306190:C>A   0.17 1.06 0.93–1.2 0.41
IL12RB1 19 rs404733:T>A   0.34 0.96 0.87–1.06 0.47
  19 rs383483:G>A   0.45 0.96 0.87–1.05 0.34
  19 rs148100486:C>T   0.0004 1.90 0.17–21.19 0.60
  19 rs438421:G>A   0.23 0.94 0.85–1.05 0.29
  19 rs376271:G>A NC_000019.10:g.18068474G>A (p.(=)) 0.01 0.89 0.59–1.34 0.58
  19 rs401502:C>G NC_000019.10:g.18069603C>G p.(R378G) 0.19 1.06 0.94–1.18 0.35
  19 rs11575934:T>C NC_000019.10:g.18075808T>C p.(Q214R) 0.09 1.10 0.93–1.3 0.28
  19 rs78041096:G>A   0.02 0.86 0.62–1.18 0.34
  19 rs376008:C>T   0.16 0.99 0.87–1.12 0.83
  19 rs116562609:T>A   0.03 1.08 0.83–1.42 0.55
  19 rs17879764:C>T   0.06 1.00 0.82–1.21 0.99
  19 rs17887070:G>A   0.15 1.01 0.89–1.15 0.86
  19 rs146102898:G>A NC_000019.10:g.18082209G>A (p.(=)) 0.004 1.42 0.71–2.84 0.32
  19 rs17887176:G>A NC_000019.10:g.18082250G>A p.(P47S) 0.06 1.00 0.82–1.22 1.00
  19 rs2305743:G>A   0.14 0.98 0.85–1.12 0.75
  19 rs436857:G>A   0.12 0.95 0.83–1.1 0.51
  19 rs393548:A>T   0.23 0.98 0.88–1.09 0.69
IFNGR2 21 rs8134145:C>A   0.47 0.98 0.9–1.08 0.72
  21 rs4986958:C>G NC_000021.8:g.34787294C>G p.(T58R) 0.19 0.96 0.84–1.09 0.50
  21 rs9808753:A>G NC_000021.9:g.33415005A>G p.(Q64R) 0.25 0.99 0.89–1.1 0.88
  21 rs7277808:C>G   0.42 0.99 0.9–1.09 0.85
  21 rs2834214:C>T   0.23 1.03 0.92–1.16 0.63
  21 rs17878711:A>G NC_000021.9:g.33427015A>G p.(K182E) 0.04 1.05 0.83–1.33 0.70
  21 rs11910627:G>C   0.06 1.08 0.88–1.32 0.45
  21 rs121913212:A>T   0.01 0.82 0.51–1.32 0.41
  21 rs41356148:C>T   0.05 0.98 0.81–1.2 0.87

Abbreviations: AA, silent and missense amino acid variants where the given position of silent variants is based on genome build hg19; CHR, chromosome; CI, confidence interval; IFN, interferon; MAF, minor allele frequency; OR, odds ratios; P, nominal P-values adjusted for gender, age and ethnic groups by logistic regression; SNP, single-nucleotide polymorphism.