Variant report

Variant	rs9295830
Chromosome Location	chr6:30044986-30044987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10947050	0.96[AFR][1000 genomes]
rs12200084	0.96[AFR][1000 genomes]
rs33959627	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3807031	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3910312	0.93[AFR][1000 genomes]
rs4711207	0.93[AFR][1000 genomes]
rs4711209	0.96[AFR][1000 genomes]
rs4713281	0.93[AFR][1000 genomes]
rs4947244	0.89[AFR][1000 genomes]
rs4959040	0.89[AFR][1000 genomes]
rs6457127	0.91[AFR][1000 genomes]
rs7767188	0.80[EUR][1000 genomes]
rs9295829	0.93[AFR][1000 genomes]
rs9348835	0.89[AFR][1000 genomes]
rs9357092	0.83[AFR][1000 genomes]
rs9366752	0.87[AFR][1000 genomes]
rs9393986	0.93[AFR][1000 genomes]
rs9393987	0.93[AFR][1000 genomes]
rs9405044	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv884049	chr6:30037353-30047403	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9295830	HLA-A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30043000-30045800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr6:30043200-30045800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:30043200-30045800	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr6:30043400-30045000	Enhancers	Dnd41	blood
5	chr6:30043600-30045400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr6:30043600-30045600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr6:30043600-30045600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:30043800-30045800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:30044200-30045800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr6:30044200-30045800	Bivalent Enhancer	HepG2	liver
11	chr6:30044600-30045800	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr6:30044600-30045800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr6:30044600-30045800	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr6:30044600-30046600	Bivalent Enhancer	Primary T cells from cord blood	blood
15	chr6:30044800-30045200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:30044800-30045800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
17	chr6:30044800-30046400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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