List of IQTLs

Click on this link to see the list of IQTLs

Fields / columns:

• Entry: Entry number per loop-SNP pair
• Loop(chr:start1-end2): Loop information. The loop is in chromosome *chr*. The first loop anchor is [*start1*, *start1 + bin*] while the second loop anchor is [*end2 - bin*, *end2*], where bin is the bin size (loop resolution).
• rsID: rsID of the IQTL SNP.
• Chromosome: Current chromosome
• SNPloc(hg19): SNP coordinate according to hg19 reference genome.
• Ref: Reference allele.
• Alt: Alternate allele.
• RASQUAL_FDR_Def: FDR (q-value) from RASQUAL default model (considering both population and allele-specific differences).
• RASQUAL_FDR_Pop: FDR (q-value) from the population specific model of RASQUAL.
• RASQUAL_FDR_AS: FDR (q-value) from the allele specific model of RASQUAL.
• Loop_b1S: *start1* (as mentioned above)
• Loop_b1E: *start1 + bin* (as mentioned above)
• Loop_b2S: *end2 - bin* (as mentioned above)
• Loop_b2E: *end2 (as mentioned above)
• Dist: Genomic distance of the loop (Loop Bin2 Start - Loop Bin1 Start)
• NumDonor: Number of donors having this contact (contact count > 0)
• SigDonor: Number of donors having this contact significant (FitHiChIP q-value < 0.01)
• NumDonor_Homo: Donors with reference homozygous genotype (Ref|Ref) having this contact (contact count > 0).
• SigDonor_Homo: Donors with reference homozygous genotype (Ref|Ref) having this contact significant (FitHiChIP q-value < 0.01).
• NumDonor_Hetero: Donors with heterozygous genotype (Ref|Alt) having this contact (contact count > 0).
• SigDonor_Hetero: Donors with heterozygous genotype (Ref|Alt) having this contact significant (FitHiChIP q-value < 0.01).
• NumDonor_AltHomo: Donors with Alternate homozygous genotype (Alt|Alt) having this contact (contact count > 0).
• SigDonor_AltHomo: Donors with Alternate homozygous genotype (Alt|Alt) having this contact significant (FitHiChIP q-value < 0.01).
• ASRead_pval: p-value by applying t-test on the allele-specific reads of the heterozygous donors.
• DICE_eQTL_CD4N: Whether the SNP is also an eQTL in CD4 Naive according to the DICE database (https://dice-database.org/)
• DICE_eGene_CD4N: If so, corresponding DICE e-Gene.
• DICE_eQTL_numCell: Out of 15 immune cell types documented in DICE, how many cell types list this SNP as eQTL.
• DICE_eQTL_numCD4TCell: Out of CD4 T cell subsets documented in DICE, how many cell types list this SNP as eQTL.
• ImmunexuT_eQTL_CD4N: Whether the SNP is also an eQTL in CD4 Naive according to the ImmunexuT database (https://www.immunexut.org/)
• ImmunexuT_eQTL_numCell: Out of all the immune cells documented in the ImmunexuT database, how many cell types list this SNP as eQTL.
• ImmunexuT_eQTL_numCD4TCell: Out of CD4 T cell subsets documented in DICE, how many cell types list this SNP as eQTL.
• Genes_loop: Genes overlapping the HiChIP loop anchors.
• WashU_Tracks (Links): Link to the WashU tracks corresponding to this IQTL (details below).
• Trend_Plots (Links): Link to the genotype and allele-specific trend plot for this IQTL (details below)

Tracks in the WashU browser:

• ATAC_Combined_Donors: ATAC-seq signal for CD4 Naive cell type (in-house data)
• ATAC_Combined_Donors_Peaks: Corresponding peaks.
• ATAC_Footprint_all: Footprint from ATAC-seq data considering all reads.
• ATAC_Footprint_NFR: Footprint from ATAC-seq data considering nucleosome free reads (NFR).
• ATAC_Footprint_NFRANDNucl: Footprint from ATAC-seq data considering nucleosome free and nuclosome containing reads.
• CTCF_CD4_Peaks_ChIP_Atlas: CTCF peaks from CD4 T cells, obtained from ChIP-ATLAS database.
• ChIP_Peaks: H3K27ac ChIP-seq peaks used for FitHiChIP loop calling in the current study.
• HiChIP_Peaks_Donors: Peaks from the HiChIP data (merged donors) called by FitHiChIP peak calling utility.
• DICE_eQTL_CD4N: DICE CD4 Naive eQTL track
• IQTL_CurrSNP: Shows the current IQTL SNP (from the SNP-loop pair).
• IQTL_CurrLoop: Shows the current IQTL associated loop (from the SNP-loop pair).
• All_IQTL_SNPs_CurrLoop: Shows all the IQTL SNPs associated with the current loop.
• All_IQTLs: Complete list of IQTL SNPs.
• ALL_Loops: Complete list of IQTL associated HiChIP loops.
• Geno_*_Aggr_FDR_FitHiChIP_L: Three tracks - for three different genotypes (in the order of reference homozygous, heterozygous and alternate homozygous), aggregated (mean) -log10(FDR) values of the FitHiChIP loops in this region.
• Geno_*_Aggr_CC_FitHiChIP_L: Same as above, except the fact that here aggregated (mean) contact counts of FitHiChIP loops are shown by color scale.
• Subsequent tracks show donor-wise FitHiChIP loops in this region.

Plots in the trend plot file:

• At the top, SNP and loop information are provided. Also, RASQUAL FDR values are mentioned in the following order: default model, population-specific model, and allele-specific model. Finally, the p-value of t-test for the allele-specific reads (from the heterozygous donors) is also mentioned.
• Plot A: genotype-dependent (X axis) variation of the raw contact counts (Y axis) of HiChIP loops.
• In the X axis, along with the genotype information, two values of the format (S/N) are provided, where N is the number of donors having this genotype and the contact (contact count > 0) while S is the number of donors having this genotype and the contact as significant (FitHiChIP q-value < 0.01).
• The white circles indicate individual donors.
• The black circles indicate mean values.
• Plot B: genotype-dependent (X axis) variation of the -log10(FDR) from FitHiChIP (Y axis). Higher value in Y axis indicates higher statistical significance.
• Plot C: genotype-dependent (X axis) variation of the normalized (by sequencing depth) contact counts (Y axis) of the corresponding HiChIP loops.
• Plot D: allele-specific reads for the heterozygous donors.
• X axis indicates allele. Beside allele information, numbers in the format (S/N)[P] are provided where S and N are the same as above, and P is the number of heterozygous donors with nonzero allele-specific reads.
• The lines between two different allele configuration shows the variation of the allele-specific reads per donor, where the donor has > 0 read for at least one allele.

List of Connectivity QTLs

Click on this link to see the list of Connectivity QTLs

Fields / columns:

• Entry: Entry number per loop-SNP pair
• Chromosome: Current chromosome
• Loop(chr:start1-end2): Loop information. The loop is in chromosome *chr*. The first loop anchor is [*start1*, *start1 + bin*] while the second loop anchor is [*end2 - bin*, *end2*], where bin is the bin size (loop resolution).
• Region1 start: Start coordinate of the first interacting broad locus.
• Region1 end: End coordinate of the first interacting broad locus.
• Region2 start: Start coordinate of the second interacting broad locus.
• Region2 end: End coordinate of the second interacting broad locus.
• Continuous: If 1, indicates that the regions 1 and 2 overlap, resulting a broad contiguous loci. Otherwise (0) the two interacting regions (containing the loops between them) are distinct.
• SNPID: SNPID
• rsID: rsID (hg19 reference genome)
• SNPloc(hg19): SNP coordinate according to hg19 reference genome.
• NumLoop: Number of HiChIP loops between these interacting broad loci which show similar genotype dependent trend of chromatin contacts, according to the given connectivity-QTL.
• WashU_Tracks (Links): Link to the WashU tracks corresponding to this IQTL (details below).
• Trend_Plots (Links): Link to the genotype and allele-specific trend plot for this IQTL (details below)

Tracks in the WashU browser:

• ATAC_Combined_Donors: ATAC-seq signal for CD4 Naive cell type (in-house data)
• ATAC_Combined_Donors_Peaks: Corresponding peaks.
• ATAC_Footprint_all: Footprint from ATAC-seq data considering all reads.
• ATAC_Footprint_NFR: Footprint from ATAC-seq data considering nucleosome free reads (NFR).
• ATAC_Footprint_NFRANDNucl: Footprint from ATAC-seq data considering nucleosome free and nuclosome containing reads.
• CTCF_CD4_Peaks_ChIP_Atlas: CTCF peaks from CD4 T cells, obtained from ChIP-ATLAS database.
• ChIP_Peaks: H3K27ac ChIP-seq peaks used for FitHiChIP loop calling in the current study.
• DICE_eQTL_CD4N: DICE CD4 Naive eQTL track
• 2D_QTL_No_LD_SNPs: Complete list of IQTL SNPs.
• 2D_QTL_No_LD_Loops: Complete list of IQTL associated HiChIP loops.
• 2D_QTL_No_LD_CurrSNP: Shows the current IQTL SNP (from the SNP-loop pair).
• 2D_QTL_No_LD_CurrLoop: Shows the current IQTL associated loop (from the SNP-loop pair).
• AllLoop_Component: All FitHiChIP loops from all the donors belonging to this region.
• Geno_*_Aggr_FDR: Three tracks - for three different genotypes (in the order of reference homozygous, heterozygous and alternate homozygous), aggregated (mean) -log10(FDR) values of the FitHiChIP loops in this region.
• Geno_*_Aggr_CC: Same as above, except the fact that here aggregated (mean) contact counts of FitHiChIP loops are shown by color scale.

Plots in the trend plot file:

• At the top, SNP and loop information are provided. Also, interacting broad loci information are given. Finally, the regression p-values with respect to genotype-dependent variation of raw (observed) HiChIP contact counts, and observed / expected HiChIP contact counts are provided.
• Plot A: genotype-dependent (X axis) variation of the raw contact counts (Y axis) of HiChIP loops.
• In the X axis, along with the genotype information, values of the format (N) are provided, where N is the number of donors having this genotype.
• Plot B: genotype-dependent (X axis) variation of the observed / expected HiChIP contact counts.