Genetics & Hepatitis B Vaccination

Table S1. List of 88 SNPs within three blocks of the human major histocompatibility complex (MHC) and selected for secondary analyses.

SNP IDa / Gene symbol / Locationb / Coordinateb / Validation status
rs9261174 c / ZNRD1 / Flanking_5’ UTR / 30104834 / Two-hit or HapMap validated
rs9261261 / ZNRD1 / Flanking_5’ UTR / 30132344 / Two-hit or HapMap validated
rs9366752 / ZNRD1 / Flanking_5’ UTR / 30132656 / Two-hit or HapMap validated
rs9261263 / ZNRD1 / Flanking_5’ UTR / 30132728 / Two-hit or HapMap validated
rs6911724 / ZNRD1 / Flanking_5’ UTR / 30133158 / Two-hit or HapMap validated
rs6911634 / ZNRD1 / Flanking_5’ UTR / 30133264 / Goldengate validated
rs259920 / ZNRD1 / Flanking_5’ UTR / 30133738 / Two-hit or HapMap validated
rs6917477 / ZNRD1 / Flanking_5’ UTR / 30133963 / Two-hit or HapMap validated
rs16896944 / ZNRD1 / Flanking_5’ UTR / 30134125 / Two-hit or HapMap validated
rs9261265 / ZNRD1 / Flanking_5’ UTR / 30134329 / Two-hit or HapMap validated
rs3132129 / ZNRD1 / Flanking_5’ UTR / 30135839 / Goldengate validated
rs3757328 / ZNRD1 / Flanking_5’ UTR / 30136331 / Two-hit or HapMap validated
rs3757329 / ZNRD1 / Flanking_5’ UTR / 30136403 / Goldengate validated
rs3757333 / ZNRD1 / Flanking_5’ UTR / 30136585 / Two-hit or HapMap validated
rs9295829 / ZNRD1 / Flanking_5’ UTR / 30136779 / Two-hit or HapMap validated
rs7770092 / ZNRD1 / Flanking_5’ UTR / 30136850 / Two-hit or HapMap validated
rs7770557 / ZNRD1 / 5’ UTR / 30137088 / Goldengate validated
rs9261269 / ZNRD1 / intron / 30138093 / Two-hit or HapMap validated
rs9261271 / ZNRD1 / intron / 30138168 / Two-hit or HapMap validated
rs9261275 / ZNRD1 / intron / 30138907 / Two-hit or HapMap validated
rs9261277 / ZNRD1 / intron / 30139070 / Two-hit or HapMap validated
rs1048412 / ZNRD1 / 3’ UTR / 30140474 / Two-hit or HapMap validated
rs3188482 / ZNRD1 / 3’ UTR / 30140652 / Two-hit or HapMap validated
rs2394956 / HLA-C / Flanking_3’ UTR / 31341435 / Two-hit or HapMap validated
rs9264523 / HLA-C / Flanking_3’ UTR / 31341737 / Two-hit or HapMap validated
rs9264531 / HLA-C / Flanking_3’ UTR / 31342218 / Two-hit or HapMap validated
rs9264532 / HLA-C / Flanking_3’ UTR / 31342360 / Two-hit or HapMap validated
rs9264582 / HLA-C / Flanking_3’ UTR / 31343795 / Two-hit or HapMap validated
rs2524099 / HLA-C / Flanking_3’ UTR / 31344030 / Two-hit or HapMap validated
rs2853950 / HLA-C / Flanking_3’ UTR / 31344154 / Goldengate validated
rs9394047 / HLA-C / Flanking_3’ UTR / 31344229 / Two-hit or HapMap validated
rs1049853 / HLA-C / 3’ UTR / 31344879 / Goldengate validated
rs4361609 / HLA-C / Flanking_5’ UTR / 31348614 / Goldengate validated
rs7759127 / HLA-C / Flanking_5’ UTR / 31348967 / Goldengate validated
rs2844621 / HLA-C / Flanking_5’ UTR / 31349516 / Goldengate validated
rs2524084 / HLA-C / Flanking_5’ UTR / 31349618 / Two-hit or HapMap validated
rs2524082 / HLA-C / Flanking_5’ UTR / 31349740 / Two-hit or HapMap validated
rs9264699 / HLA-C / Flanking_5’ UTR / 31349912 / Two-hit or HapMap validated
rs9380232 / HLA-C / Flanking_5’ UTR / 31350720 / Two-hit or HapMap validated
rs3132486 / HLA-C / Flanking_5’ UTR / 31351149 / Goldengate validated
rs3132485 / HLA-C / Flanking_5’ UTR / 31351368 / Two-hit or HapMap validated
rs2844613 / HLA-C / Flanking_5’ UTR / 31351825 / Two-hit or HapMap validated
rs2844612 / HLA-C / Flanking_5’ UTR / 31351950 / Two-hit or HapMap validated
rs9264731 / HLA-C / Flanking_5’ UTR / 31352047 / Goldengate validated
rs9264733 / HLA-C / Flanking_5’ UTR / 31352193 / Two-hit or HapMap validated
rs2524070 / HLA-C / Flanking_5’ UTR / 31352499 / Goldengate validated
rs9264742 / HLA-C / Flanking_5’ UTR / 31352595 / Two-hit or HapMap validated
rs2524069 / HLA-C / Flanking_5’ UTR / 31352768 / Goldengate validated
rs2524068 / HLA-C / Flanking_5’ UTR / 31353040 / Two-hit or HapMap validated
rs6457374 / HLA-C / Flanking_5’ UTR / 31380240 / Goldengate validated
rs9264942 c / HLA-C / Flanking_5’ UTR / 31382359 / Two-hit or HapMap validated
rs2523685 d / HCP5 / Flanking_5’ UTR / 31534235 / Goldengate validated
rs6930572 / HCP5 / Flanking_5’ UTR / 31536148 / Two-hit or HapMap validated
rs2395029 c / HCP5 / coding / 31539759 / Goldengate validated
rs2395030 / HCP5 / 3’ UTR / 31539853 / Two-hit or HapMap validated
rs2284178 / HCP5 / 3’ UTR / 31540104 / Goldengate validated
rs11757571 / HCP5 / 3’ UTR / 31540766 / Two-hit or HapMap validated
rs11759988 / HCP5 / 3’ UTR / 31540840 / Two-hit or HapMap validated
rs3094013 / HCP5 / Flanking_3’ UTR / 31542345 / Two-hit or HapMap validated
rs2516518 / HCP5 / Flanking_3’ UTR / 31543098 / Two-hit or HapMap validated
rs4713466 / HCP5 / Flanking_3’ UTR / 31543848 / Two-hit or HapMap validated
rs2523676 / HCP5 / Flanking_3’ UTR / 31543970 / Goldengate validated
rs1121800 / LTA / Flanking_5’ UTR / 31643053 / Two-hit or HapMap validated
rs2844484 / LTA / Flanking_5’ UTR / 31644203 / Goldengate validated
rs2844482 / LTA / Flanking_5’ UTR / 31647746 / Goldengate validated
rs2239704 / LTA / 5’ UTR / 31648120 / Two-hit or HapMap validated
rs909253 / LTA / intron / 31648292 / Goldengate validated
rs2229094 / LTA / coding / 31648535 / Two-hit or HapMap validated
rs3093542 / LTA / intron / 31648672 / Two-hit or HapMap validated
rs2229092 / LTA / coding / 31648736 / Two-hit or HapMap validated
rs3093544 / LTA / 3’ UTR / 31649758 / Two-hit or HapMap validated
rs1799964 / LTA / Flanking_3’ UTR / 31650287 / Goldengate validated
rs1799724 / LTA / Flanking_3’ UTR / 31650461 / non-validated
rs361525 / TNF / Flanking_5’ UTR / 31651080 / non-validated
rs3093662 / TNF / intron / 31652168 / Goldengate validated
rs769177 / LTB / Flanking_3’ UTR / 31655590 / Two-hit or HapMap validated
rs9268614 / HLA-DRA / Flanking_5’ UTR / 32510756 / Two-hit or HapMap validated
rs7194 / HLA-DRA / 3’ UTR / 32520458 / Goldengate validated
rs9270986 / HLA-DRB1 / Flanking_5’ UTR / 32682038 / Two-hit or HapMap validated
rs615672 / HLA-DRB1 / Flanking_5’ UTR / 32682149 / Two-hit or HapMap validated
rs3129763 / HLA-DQA1 / Flanking_5’ UTR / 32698903 / Goldengate validated
rs9272346 / HLA-DQA1 / Flanking_5’ UTR / 32712350 / Goldengate validated
rs6928482 / HLA-DQB1 / Flanking_3’ UTR / 32734227 / Goldengate validated
rs9275141 / HLA-DQB1 / Flanking_5’ UTR / 32759095 / Goldengate validated
rs6457617 / HLA-DQB1 / Flanking_5’ UTR / 32771829 / Goldengate validated
rs6457663 / HLA-DQB2 / Flanking_5’ UTR / 32847290 / Two-hit or HapMap validated
rs11244 / HLA-DOB / 3’ UTR / 32888701 / Goldengate validated
rs3128955 / HLA-DPA1 / Flanking_3’ UTR / 33129170 / Two-hit or HapMap validated

a All have successful genotyping in up to 280 patients with sufficient amount of DNA. The reference sequence (rs) numbers correspond to those assigned by NCBI dbSNP (version 128, last accessed in October 2008). A space is introduced between MHC blocks, which are mapped to the short arm of chromosome 6 (6p21.3). Note that MHC class II SNPs are chosen more selectively, based on their tagging of HLA alleles associated with various autoimmune diseases (

bSNP location is relative to each gene, while the coordinate corresponds the chromosome 6 sequences in human genome build version 36 (last accessed in October 2008).

c These SNPs have been implicated in a genome-wide association study conducted at the Center for HIV/AIDSVaccine Immunology ( as important to HIV-1 infection (see text).

dThis SNP (rs2523685) is provisionally associated with antibody responses (see Figure 1 and text).

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Genetics & Hepatitis B Vaccination

Table S2. Distribution [n (%)] of select HLA class II variants in 335 patients stratified by race/ethnicity, HIV-1 infection, and antibody (Ab) response.

By race/ethnicitya / By HIV-1 infection / By Ab response profilea
Black, non-Hispanic / Hispanic / All othersa / Uninfected / Infected / HR / MR / NR
Total no. of subjects / 93 / 229 / 13 / 80 / 255 / 97 / 160 / 78
By allele groupsb
DRB1*03c / 28 (30.1) / 37 (16.2) / 6 (46.2) / 13 (16.3) / 58 (22.7) / 15 (15.5) / 33 (20.6) / 23 (29.5)
DRB1*04d / 8 (8.6) / 67 (29.3) / 1 (7.7) / 32 (40.0) / 44 (17.3) / 21 (21.7) / 38 (23.8) / 17 (21.8)
DRB1*07 / 16 (17.2) / 53 (23.1) / 2 (15.4) / 15 (18.8) / 56 (22.0) / 14 (14.4) / 36 (22.5) / 21 (26.9)
DRB1*08 / 14 (15.1) / 36 (15.7) / 1 (7.7) / 16 (20.0) / 35 (13.7) / 22 (22.7) / 22 (13.8) / 7 (9.0)
DRB1*15 c / 18 (19.4) / 47 (20.5) / 5 (38.5) / 15 (18.8) / 55 (21.6) / 26 (26.9) / 30 (18.8) / 14 (17.9)
DQB1*02c / 35 (37.6) / 74 (32.3) / 7 (53.8) / 21 (26.3) / 95 (37.3) / 26 (26.8) / 56 (35.0) / 34 (43.6)
By major allelese
DRB1*0301 / 15 (16.1) / 23 (10.0) / 5 (38.5) / 7 (8.8) / 36 (14.1) / 10 (10.3) / 20 (12.5) / 13 (16.7)
DRB1*0302 / 11 (11.8) / 14 (6.1) / 1 (7.7) / 6 (7.5) / 20 (7.8) / 4 (4.1) / 13 (8.1) / 9 (11.5)
DRB1*0407d / 0 / 19 (8.3) / 0 / 15 (18.8) / 4 (1.6) / 7 (7.2) / 10 (6.3) / 2 (2.6)
DRB1*0801 / 1 (1.1) / 7 (3.1) / 1 (7.7) / 4 (5.0) / 5 (2.0) / 4 (4.1) / 4 (2.5) / 1 (1.3)
DRB1*0802d / 1 (1.1) / 15 (6.6) / 0 / 8 (10.0) / 8 (3.1) / 5 (5.1) / 8 (5.0) / 3 (3.8)
DRB1*0804f / 10 (10.8) / 11 (4.8) / 0 / 3 (3.8) / 18 (7.1) / 11 (11.3) / 9 (5.6) / 1 (1.3)
DRB1*1602 / 0 / 13 (5.7) / 0 / 5 (6.3) / 8 (3.1) / 4 (4.1) / 8 (5.0) / 1 (1.3)
DQA1*0103f / 16 (17.2) / 21 (9.2) / 0 / 2 (2.5) / 35 (13.7) / 11 (11.3) / 15 (9.4) / 11 (14.1)
DQA1*0301d / 1 (1.1) / 50 (21.8) / 2 (15.4) / 24 (30.0) / 29 (11.4) / 15 (15.5) / 26 (16.3) / 12 (15.4)
DQB1*0201 / 17 (18.3) / 30 (13.1) / 5 (38.5) / 8 (10.0) / 44 (17.3) / 12 (12.4) / 24 (15.0) / 16 (20.5)
DQB1*0202 / 22 (23.7) / 49 (21.4) / 2 (15.4) / 16 (20.0) / 57 (22.4) / 17 (17.5) / 36 (22.5) / 20 (25.6)
DQB1*0301 / 79 (34.5) / 27 (29.0) / 2 (15.4) / 20 (25.0) / 88 (34.5) / 32 (33.0) / 57 (35.6) / 19 (24.4)
DQB1*0503 f / 4 (4.3) / 10 (4.4) / 1 (7.7) / 1 (1.3) / 14 (5.5) / 4 (4.1) / 7 (4.4) / 4 (5.1)
DQB1*0603 f / 11 (11.8) / 18 (7.9) / 0 / 0 / 29 (11.4) / 10 (10.3) / 11 (6.9) / 8 (10.3)
By major haplotypesd
DRB1*03-DQB1*02 / 11 (11.8) / 23 (10.0) / 4 (30.8) / 7 (8.8) / 36 (14.1) / 11 (11.3) / 20 (12.5) / 12 (15.4)
DRB1*03-DQB1*04 / 11 (11.8) / 11 (4.8) / 1 (7.7) / 6 (7.5) / 17 (6.7) / 3 (3.1) / 12 (7.5) / 8 (10.3)
DRB1*07-DQB1*02 / 15 (16.1) / 48 (21.0) / 2 (15.4) / 13 (16.3) / 52 (20.4) / 13 (13.4) / 33 (20.6) / 19 (24.4)
DRB1*08-DQB1*03 f / 11 (11.8) / 10 (4.4) / 1 (7.7) / 2 (2.5) / 20 (7.8) / 12 (12.4) / 8 (5.0) / 2 (2.6)
DRB1*08-DQB1*04 / 0 / 26 (11.4) / 0 / 12 (15.0) / 14 (5.5) / 8 (8.2) / 13 (8.1) / 5 (6.4)
DRB1*0302-DQB1*0402 / 10 (10.8) / 11 (4.8) / 1 (7.7) / 6 (7.5) / 16 (6.3) / 3 (3.1) / 12 (7.5) / 7 (9.0)
DRB1*0407-DQB1*0302e / 0 / 17 (7.4) / 0 / 14 (17.5) / 3 (1.2) / 6 (6.2) / 9 (5.6) / 2 (2.6)
DRB1*0804-DQB1*0301f / 9 (9.7) / 8 (3.5) / 0 / 1 (1.3) / 16 (6.3) / 9 (9.3) / 7 (4.4) / 1 (1.3)

aAs defined in Table 1. Non-responders (NR) have serum Ab concentrations <10 mIU/mL at week 28 (4 wks after last dose of vaccination); medium responders (MR) at 10-1000 mIU/mL; high responders (HR) >1,000 mIU/mL.

b Restricted to those putatively associated with differential Ab responses (univariate P ≤0.050), including those (e.g., DRB1*04 and DRB1*15) detected in analyses of 255 HIV patients alone; DRB1*0701 is not listed separately because it is the only allele in the DRB1*07 group.

c DRB1*03 and DRB1*07 are in strong linkage disequilibrium with DQB1*02 (see text), while DRB1*15 is found exclusively on the DRB1*15-DQB1*06 haplotype.

d These are enriched in the HIV-1 seronegative (uninfected) volunteers (univariate P ≤0.050).

e Restricted to those that may explain associations attributable to alleles or allele groups; two haplotypes are omitted because DRB1*03-DQB1*02 = DRB1*0301-DQB1*0201 and DRB1*07-DQB1*02 = DRB1*0701-DQB1*0202.

f These are enriched in the HIV-1 seropositive (infected) patients (univariate P ≤0.050).

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