Table 2 Analysis of GWAS SNPs located in DHSs on MHC region from human, chimpanzee, and macaque fibroblasts
StartEndSNPSpecies-specificSNP associating with disease (GWAS)Mapped geneReported geneDHS target gene from HI-C dataeQTL
3084815430848345rs7756521CgainHIV-1 controlDDR1DDR1, VARS2, DPCR1DDR1DDR1
3119738131197644rs3130941HlossIgE levelsTRNAI25HLA-C, HCG27HCG22HCG27
3123372531241873rs2074488CommonChronic obstructive pulmonary diseaseHLA-CHLA-CHLA-C, POU5F1PSORS1C3, POU5F1
3132229831322508rs3819299ClossPlatelet countsHLA-BHLA-BHLA-B, HLA-Cnone
3143138531431813rs2395029ClossHIV-1 controlHCP5HLA-B, HCP5HLA-C, HLA-B, MICBMICB (moderate negative)
3154206331542726rs1799964CommonCrohn’s diseaseLTA;TNFLTA,HLA-DQA2,TNF,LST1,LTBHLA-C, HLA-BLST1
3158735031591070rs2736172CommonPsychosis (atypical)PRRC2A; SNORA38MICB, TNFPRRC2A, BAG6, ATF6BBAG6, ATF6B, PRRC2A
3163160031634790rs3130618CommonFebrile seizures (MMR vaccine-related)GPANK1GPANK1HLA-B, HLA-C, GPANK1CYP21A2
3216529132165513rs2071278CommonComplement C3 and C4 levelsNOTCH4HLA-DRAHLA-DRA, CYP21A2CYP21A2, C4B
3259072532591250rs9271588, rs3129763, rs34831921MlossSystemic sclerosis, sum neutrophil eosinophil counts, parental lifespan Sjogren’s syndromeTRNAI25HLA-DRA, HLA-DQA1, HLA-DRB1 HLA-DRB5, HLA-DRB6HLA-DQA1HLA-DRB6
3260580032605972rs2187668HgainAutoimmune hepatitis type 1, systemic lupus erythematosus, nephropathy, immunoglobulin A, celiac diseaseHLA-DQA1HLA-DQA1, HLA-DR3, HLA-DRB1, HLA-DQB1HLA-DQA1, HLA-DRB1, HLA-DQB1CYP21A1P
3263367832634221rs9274477ClossNarcolepsy (age of onset)HLA-DQB1NRHLA-DQB1HLA-DQB2
3278184232785278rs2071747, rs7383287CommonLung cancer in ever smokers, Schizophrenia, strep throatHLA-DOB,HLA-DOBHLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRA, HLA-DRB1, HLA-DRB5, HLA-DRB9none
3282006532823157rs17220241CommonBlood protein levelsTAP1, PSMB9HLA-Z, PSMB8, PSMB9, TAP1, TAP2, XXbac-BPG246D15.9,HLA-DMA, HLA-DMB, HLA-DPA1, HLA-DPB1, HLA-DPB2, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DRA, HLA-DRB1, PSMB8, PSMB9, TAP1, TAP2, XXbac-BPG246D15.9none
3291311032913295rs1480380MlossAutism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophreniaTRNAI25NRHLA-DRB1, HLA-DQA1, HLA-DMA, HLA-DMB, BRD2HLA-DMA, BRD2, HLA-DMB (combined eQTL)
3308625533087057rs1883414MlossIGA nephropathyTRNAI25HLA-DPA1, HLA-DPB1, HLA-DPB2HLA-DPA1, HLA-DPB1, HLA-DPB2none