Table 1.
Loci Showing Genome-wide Significant Association with Either AD or Psoriasis Defined by All Three Methods of Comparative Analysis
| Chr Band | Reference SNV Number(s) | Position (hg19) | Nearest Gene(s) or Transcript(s) | Effect Observed in GW Analyses |
Estimated Odds Ratio (95% CI) |
Previous Report(s) of Association at This Locus | |
|---|---|---|---|---|---|---|---|
| AD | Psoriasis | ||||||
| 1p31.3 | rs77614545 (del) | 67749581 | retro-DNAJB6 and IL23R (MIM 607562) | psoriasis | 0.99 (0.92–1.07) | 1.21 (1.15–1.28) | psoriasis: 1p31.3 locus, IL28RA21,24,40 |
| 1q21.3a |
rs55879323 | 152168740 | within FLG-AS1 | opposing | 0.76 (0.70–0.82) | 1.05 (1.00–1.12) | AD and psoriasis: 1q21.3 locus, HRNR, FLG;41FLG;20,42LCE3B, LCE3C,18LCE gene cluster;17LCE3D24 |
| rs11205006, rs12144049 | 152440176, 152440910 | RP1-91G5.3, CRNN (MIM 611312), LCE5A (MIM 612619) | AD | 1.52 (1.41–1.64), 1.53 (1.42–1.64) | 0.97 (0.92–1.03), 0.98 (0.92–1.03) | AD: 1q21.3 locus, HRNR, FLG;41FLG20,42 | |
| rs471144 | 152454255 | LCE5A (MIM 612619) | AD | 1.54 (1.37–1.73) | 1.03 (0.94–1.14) | AD: 1q21.3 locus, HRNR, FLG;41FLG20,42 | |
| rs10888499 | 152532742 | LCE3E (MIM 612617) | AD | 1.49 (1.38–1.61) | 0.98 (0.93–1.04) | AD: 1q21.3 locus, HRNR, FLG;41FLG20,42 | |
| rs4112788 | 152551276 | LCE3D (MIM 612616) | psoriasis | 0.97 (0.90–1.05) | 1.22 (1.15–1.28) | psoriasis: LCE gene cluster;17LCE3D24 | |
| rs1581803 | 152592281 | LCE3A (MIM 612613) | psoriasis | 0.97 (0.90–1.04) | 1.22 (1.15–1.30) | psoriasis: LCE gene cluster17 | |
| rs77199844 (del) | 152757094 | LCE1E (MIM 612607) | [AD] | 2.01 (1.72–2.35) | 1.16 (1.01–1.33) | AD: 1q21.3 locus, HRNR, FLG;41FLG20,42 psoriasis: LCE gene cluster17 |
|
| rs4363385 | 152989321 | SNORA31, SPRR3 (MIM 182271), SPRR1B (MIM 182266) | [opposing] | 1.23 (1.15–1.32) | 0.89 (0.85–0.94) | AD: SPRR3 repeat number variant43 | |
| 2p16.1 | rs35741374 | 61072567 | within lincRNA AC010733.4 | psoriasis | 1.09 (1.01–1.63) | 1.20 (1.15–1.27) | psoriasis: REL;24NR23 |
| 2q31.2 | rs62176107 | 179300971 | exonic PRKRA and within miRNA548n and AC009948.5 | opposing | 0.55 (0.46–0.65) | 1.42 (1.32–1.53) | – |
| 5q31.1a |
rs1295686 | 131952222 | intronic IL13 (MIM 147683) and within AC004041.2 | [opposing] | 1.27 (1.17–1.38) | 0.88 (0.82–0.94) | AD and psoriasis: IL13;21KIF3A, IL13;22KIF3A, IL4, IL13-RAD50;10 multiple effect locus RAD50/IL13;20C5orf56 |
| rs6596086 | 131995843 | intronic RAD50 (MIM 604040) | opposing | 1.30 (1.20–1.41) | 0.85 (0.8–0.91) | AD and psoriasis: IL13-RAD50;10 multiple effect locus RAD50/IL1320 | |
| 5q33.1 | rs17728338 | 150478318 | ANXA6 (MIM 114070) | opposing | 0.70 (0.59–0.84) | 1.77 (1.61–1.95) | psoriasis: TNIP121,42 |
| 5q33.3 |
rs10515778, rs7715173, rs7719425b | 158658012, 158664631, 158670938 | within CTB-11I22.1 | psoriasis | 1.07 (0.98–1.17) | 1.29 (1.21–1.38) | psoriasis: 5q33.3 locus, IL12B17,21,24,44; AD: PTTG142 |
| rs11135056, rs4921442b | 158687281, 158694100 | intronic UBLCP1 (MIM 609867) | psoriasis | 0.97 (0.89–1.05) | 1.45 (1.35–1.56) | ||
| rs2546890 | 158759900 | within AC008697.1 | psoriasis | 1.01 (0.94–1.06) | 1.39 (1.32–1.47) | ||
| rs5872599 (indel) | 158859989 | lincRNA AC008703.1, IL12B (MIM 161561) | psoriasis | 0.82 (0.73–0.93) | 1.54 (1.45–1.64) | ||
| 6q21 |
rs9487605 | 111582885 | intronic KIAA1919 | psoriasis | 1.06 (0.98–1.14) | 1.27 (1.20–1.35) | – |
| rs240993 | 111673714 | intronic REV3L (MIM 602776) | psoriasis | 1.05 (0.97–1.13) | 1.29 (1.22–1.36) | – | |
| rs9481169 | 111929862 | TRAF3IP2 (MIM 607043) | psoriasis | 0.98 (0.86–1.11) | 1.58 (1.45–1.72) | psoriasis and psoriatic arthritis: TRAF3IP224,44,45 | |
| 6q23.2 | rs643177, rs582757b | 138195693, 138197824 | TNFAIP3 (MIM 610669) | psoriasis | 1.05 (0.97–1.14) | 1.27 (1.20–1.34) | psoriasis: TNFAIP321,24 |
| 11q13.5 | rs2212434, rs7126418b | 76281593, 76292573 | c11orf30 (MIM 608574) | AD | 1.29 (1.21–1.39) | 1.05 (1.00–1.11) | AD: c11orf30-LRRC32;10,41c11orf30;22 11q13 locus20 |
| 12q13.3 | rs36207871 (del) | 56684496 | intronic CS (MIM 118950) | psoriasis | 0.94 (0.83–1.06) | 1.47 (1.33–1.67) | psoriasis: 12q13.3 locus, IL23A, STAT2;21IL23A24 |
| rs11575234 | 56744276 | intronic STAT2 (MIM 600556) | psoriasis | 0.90 (0.79–1.02) | 1.47 (1.32–1.64) | psoriasis: STAT221 | |
Genome-wide significance is defined as CCMA Tmax > 6 and MANTRA BFDP < 0.05 with PO = 1/999 and multinomial model p < 10−8; genes and transcripts identified from UCSC Genome Browser Human Feb. 2009 (GRCh37/hg19) Assembly accessed 21 March 2014; this variant of FLG-AS1 extends across HRHR and FLG; RP1-91G5.3 extends across CRNN; AC004041.2 extends across RAD50 and IL13; CTB-11I22.1 overlaps RNF145.
1q21.3 and 5q31.1 were further investigated via stepwise conditional analysis (the results are shown in Table 2); square brackets indicate results from the univariate analysis that were subsequently accounted for by other nearby variants when examined by stepwise conditional analysis.
Multiple SNVs are assigned to the same LD block but odds ratios and 95% CI are presented only for the first SNV.