Variant report

Variant	rs2523431
Chromosome Location	chr6:29484215-29484216
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1233480	0.86[EUR][1000 genomes]
rs1233493	0.98[EUR][1000 genomes]
rs1233494	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1234844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2023463	0.98[EUR][1000 genomes]
rs2143668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2523432	0.92[EUR][1000 genomes]
rs2523443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2746149	0.98[EUR][1000 genomes]
rs2746150	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094569	0.89[EUR][1000 genomes]
rs404240	0.91[EUR][1000 genomes]
rs408623	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3424039	chr6:29439297-29504564	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv883528	chr6:29447724-29494897	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv883529	chr6:29464365-29494897	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv966616	chr6:29479346-29495253	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2523431	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs2523431	HLA-C	Cis_chr	lymphoblastoid	RTeQTL
rs2523431	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs2523431	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29468600-29496200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:29483400-29484600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:29483400-29484800	Enhancers	HMEC	breast
4	chr6:29483600-29484400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:29483600-29484800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:29483600-29484800	Enhancers	NHEK	skin
7	chr6:29483800-29484600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:29483800-29484600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr6:29483800-29484600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:29484000-29484400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:29484000-29484400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:29484000-29484400	Enhancers	Hela-S3	cervix
13	chr6:29484000-29484600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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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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