The HLA gene regulates our acquired immune system. It is what helps our body identify foreign antigens (bacteria, fungi, viruses) and determine what type of white blood cells and antibodies should be produced. Depending on our HLA type we are more or less resistant to certain diseases and infections. HLA also influences our risk of developing autoimmune diseases like diabetes, multiple sclerosis, rheumatism, arthritis, hypothyroidism, psoriasis, Celiac disease, Crohn's disease, fibromyalgia, and so on.
Class I HLA (A, B and C) deal with intracellular immunity, i.e. mostly viruses and some bacteria (e.g. Chlamydia, Rickettsia, Mycobacteria, Mycoplasma). Class II HLA (DM, DO, DP, DQ, DR) fight off extracellular pathogens - mostly bacteria and fungi. HLA DM to DQ have little diversity, so the main determinant of extracellular immunity between individuals is above all HLA-DR. HLA-DR is subdivided in HLA-DRA (3 variants) and HLA-DRB (439 variants), but all useful variations are found within HLA-DRB, which has 23 types usually in European/Caucasian people. The short-hand HLA-DR always refers to HLA-DRB.
You can compare the distribution of HLA-DR alleles by country to get a better idea of where each type is more common. To better visualize regional variations, I have started making maps for each HLA-DR type. Here are those that I have already made: HLA-DR1, HLA-DR3, HLA-DR4, HLA-DR7, HLA-DR11, HLA-DR15, HLA-DR16.
You can know your HLA types through a blood test, i.e. serotype (ask your doctor), or checking the raw from your DNA, i.e. genotype, if you tested with 23andMe, and in some cases also with Geno 2.0 or FamilyFinder. Some alleles are not tested by any of the three companies though. I have found a list of SNPs for all common European types, but unfortunately I do not know which allele is positive for some SNPs. If some of you have more information, make sure to share it.
There are subtypes for each HLA-DR type, although most of them have only one common subtype in Europe. HLA-DRB*0101 means essentially the same as HLA-DR1. To be more accurate it is subtype 1 of HLA-DR1, but it is the only subtype found in Europe. The highest diversity of subtypes in found within HLA-DR4, although non-Mediterranean Europeans usually belong to HLA-DRB*0401. The positive allele is indicated in brackets/parentheses. You will need to be positive for all SNPs listed in the same row to belong to one HLA-DR type. Each person normally belongs to two HLA-DR types (although it is possible to have twice the same). The most common subtypes are indicated in bold.
I have tried to geographically match the colours of HLA types to the colours I used for Y-DNA haplogroups. For example, HLA-DR9 is most common in North Asia and among Finno-Ugric people, so I used purple like for Y-haplogroup N1c. HLA-DR11 peaks in West Asia, Greece and Italy, so I used green like for Y-haplogroup J2. I couldn't always find a correlation with Y-DNA, so I sometime used colours used for mtDNA or autosomal maps, as in HLA-DR15 which is orange like the ANE admixture.
[TABLE="class: grid, width: 600, align: left"]
[TR]
[TD]HLA-DR Type
[/TD]
[TD]SNP 1[/TD]
[TD]SNP 2[/TD]
[TD]SNP 3[/TD]
[/TR]
[TR]
[TD][/TD]
[TD][/TD]
[TD][/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*0101
[/TD]
[TD]rs4947332 (T)[/TD]
[TD]rs6457614 (G)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*0301
[/TD]
[TD]rs2040410 (A)[/TD]
[TD][/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*0401[/TD]
[TD]rs6910071 (G)[/TD]
[TD]rs3817964 (A)[/TD]
[TD]rs660895 (G)[/TD]
[/TR]
[TR]
[TD]HLA-DRB*0402
[/TD]
[TD]rs3130071 (T)[/TD]
[TD]rs416352 (T)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*0403[/TD]
[TD]rs7454108 (C)[/TD]
[TD]rs206765[/TD]
[TD]rs399604[/TD]
[/TR]
[TR]
[TD]HLA-DRB*0404
[/TD]
[TD]rs2736157 (G)[/TD]
[TD]rs3115572 (C)[/TD]
[TD]rs2395533[/TD]
[/TR]
[TR]
[TD]HLA-DRB*0405
[/TD]
[TD]rs1057149 (A)[/TD]
[TD][/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*0407[/TD]
[TD]rs7774197 (C)[/TD]
[TD]rs417812[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*0701[/TD]
[TD]rs7745002[/TD]
[TD]rs2647087[/TD]
[TD]rs241398[/TD]
[/TR]
[TR]
[TD]HLA-DRB*0801[/TD]
[TD]rs7743506[/TD]
[TD][/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*0901
[/TD]
[TD]rs2395185 (T)[/TD]
[TD]rs2516049 (C)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1001[/TD]
[TD]rs4148871 (A)[/TD]
[TD]rs2071538 (A)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1101[/TD]
[TD]rs434841 (A)[/TD]
[TD]rs1061172[/TD]
[TD]rs5875439 (I)[/TD]
[/TR]
[TR]
[TD]HLA-DRB*1103[/TD]
[TD]rs4639334 (A)[/TD]
[TD]rs412735[/TD]
[TD]rs210180 (A)[/TD]
[/TR]
[TR]
[TD]HLA-DRB*1104
[/TD]
[TD]rs4713607 (G)[/TD]
[TD]rs12664430 (T)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1201[/TD]
[TD]rs6901541 (C)[/TD]
[TD]rs6916742[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1301[/TD]
[TD]rs2395173 (A)[/TD]
[TD]rs2157051 (C)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1302[/TD]
[TD]rs4434496 (T)[/TD]
[TD]rs6901541 (C)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1303
[/TD]
[TD]rs424232 (T)[/TD]
[TD]rs2050191 (A)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1401[/TD]
[TD]rs2763979 (T)[/TD]
[TD]rs1794265 (C)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1404[/TD]
[TD]rs805262 (T)[/TD]
[TD]rs1794265 (C)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1501[/TD]
[TD]rs3135388 (T)[/TD]
[TD][/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1601[/TD]
[TD]rs3129891 (A)[/TD]
[TD]rs6923504 (G)[/TD]
[TD][/TD]
[/TR]
[/TABLE]
Note that HLA-DR2 doesn't exist anymore. It was split into DR15 and DR16. Likewise HLA-DR5 was split in HLA-DR11 and HLA-DR12, while HLA-DR6 was divided in HLA-DR13 and HLA-DR14.
Depending on reading directions your DNA test, the letters of the alleles might different. Just remember that C=G and A=T.
Class I HLA (A, B and C) deal with intracellular immunity, i.e. mostly viruses and some bacteria (e.g. Chlamydia, Rickettsia, Mycobacteria, Mycoplasma). Class II HLA (DM, DO, DP, DQ, DR) fight off extracellular pathogens - mostly bacteria and fungi. HLA DM to DQ have little diversity, so the main determinant of extracellular immunity between individuals is above all HLA-DR. HLA-DR is subdivided in HLA-DRA (3 variants) and HLA-DRB (439 variants), but all useful variations are found within HLA-DRB, which has 23 types usually in European/Caucasian people. The short-hand HLA-DR always refers to HLA-DRB.
You can compare the distribution of HLA-DR alleles by country to get a better idea of where each type is more common. To better visualize regional variations, I have started making maps for each HLA-DR type. Here are those that I have already made: HLA-DR1, HLA-DR3, HLA-DR4, HLA-DR7, HLA-DR11, HLA-DR15, HLA-DR16.
You can know your HLA types through a blood test, i.e. serotype (ask your doctor), or checking the raw from your DNA, i.e. genotype, if you tested with 23andMe, and in some cases also with Geno 2.0 or FamilyFinder. Some alleles are not tested by any of the three companies though. I have found a list of SNPs for all common European types, but unfortunately I do not know which allele is positive for some SNPs. If some of you have more information, make sure to share it.
There are subtypes for each HLA-DR type, although most of them have only one common subtype in Europe. HLA-DRB*0101 means essentially the same as HLA-DR1. To be more accurate it is subtype 1 of HLA-DR1, but it is the only subtype found in Europe. The highest diversity of subtypes in found within HLA-DR4, although non-Mediterranean Europeans usually belong to HLA-DRB*0401. The positive allele is indicated in brackets/parentheses. You will need to be positive for all SNPs listed in the same row to belong to one HLA-DR type. Each person normally belongs to two HLA-DR types (although it is possible to have twice the same). The most common subtypes are indicated in bold.
I have tried to geographically match the colours of HLA types to the colours I used for Y-DNA haplogroups. For example, HLA-DR9 is most common in North Asia and among Finno-Ugric people, so I used purple like for Y-haplogroup N1c. HLA-DR11 peaks in West Asia, Greece and Italy, so I used green like for Y-haplogroup J2. I couldn't always find a correlation with Y-DNA, so I sometime used colours used for mtDNA or autosomal maps, as in HLA-DR15 which is orange like the ANE admixture.
[TABLE="class: grid, width: 600, align: left"]
[TR]
[TD]HLA-DR Type
[/TD]
[TD]SNP 1[/TD]
[TD]SNP 2[/TD]
[TD]SNP 3[/TD]
[/TR]
[TR]
[TD][/TD]
[TD][/TD]
[TD][/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*0101
[/TD]
[TD]rs4947332 (T)[/TD]
[TD]rs6457614 (G)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*0301
[/TD]
[TD]rs2040410 (A)[/TD]
[TD][/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*0401[/TD]
[TD]rs6910071 (G)[/TD]
[TD]rs3817964 (A)[/TD]
[TD]rs660895 (G)[/TD]
[/TR]
[TR]
[TD]HLA-DRB*0402
[/TD]
[TD]rs3130071 (T)[/TD]
[TD]rs416352 (T)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*0403[/TD]
[TD]rs7454108 (C)[/TD]
[TD]rs206765[/TD]
[TD]rs399604[/TD]
[/TR]
[TR]
[TD]HLA-DRB*0404
[/TD]
[TD]rs2736157 (G)[/TD]
[TD]rs3115572 (C)[/TD]
[TD]rs2395533[/TD]
[/TR]
[TR]
[TD]HLA-DRB*0405
[/TD]
[TD]rs1057149 (A)[/TD]
[TD][/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*0407[/TD]
[TD]rs7774197 (C)[/TD]
[TD]rs417812[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*0701[/TD]
[TD]rs7745002[/TD]
[TD]rs2647087[/TD]
[TD]rs241398[/TD]
[/TR]
[TR]
[TD]HLA-DRB*0801[/TD]
[TD]rs7743506[/TD]
[TD][/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*0901
[/TD]
[TD]rs2395185 (T)[/TD]
[TD]rs2516049 (C)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1001[/TD]
[TD]rs4148871 (A)[/TD]
[TD]rs2071538 (A)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1101[/TD]
[TD]rs434841 (A)[/TD]
[TD]rs1061172[/TD]
[TD]rs5875439 (I)[/TD]
[/TR]
[TR]
[TD]HLA-DRB*1103[/TD]
[TD]rs4639334 (A)[/TD]
[TD]rs412735[/TD]
[TD]rs210180 (A)[/TD]
[/TR]
[TR]
[TD]HLA-DRB*1104
[/TD]
[TD]rs4713607 (G)[/TD]
[TD]rs12664430 (T)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1201[/TD]
[TD]rs6901541 (C)[/TD]
[TD]rs6916742[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1301[/TD]
[TD]rs2395173 (A)[/TD]
[TD]rs2157051 (C)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1302[/TD]
[TD]rs4434496 (T)[/TD]
[TD]rs6901541 (C)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1303
[/TD]
[TD]rs424232 (T)[/TD]
[TD]rs2050191 (A)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1401[/TD]
[TD]rs2763979 (T)[/TD]
[TD]rs1794265 (C)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1404[/TD]
[TD]rs805262 (T)[/TD]
[TD]rs1794265 (C)[/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1501[/TD]
[TD]rs3135388 (T)[/TD]
[TD][/TD]
[TD][/TD]
[/TR]
[TR]
[TD]HLA-DRB*1601[/TD]
[TD]rs3129891 (A)[/TD]
[TD]rs6923504 (G)[/TD]
[TD][/TD]
[/TR]
[/TABLE]
Note that HLA-DR2 doesn't exist anymore. It was split into DR15 and DR16. Likewise HLA-DR5 was split in HLA-DR11 and HLA-DR12, while HLA-DR6 was divided in HLA-DR13 and HLA-DR14.
Depending on reading directions your DNA test, the letters of the alleles might different. Just remember that C=G and A=T.
Last edited: