Variant report

Variant	rs13207082
Chromosome Location	chr6:27251379-27251380
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs13191227	1.00[CEU][hapmap]
rs13195040	0.90[CEU][hapmap];1.00[TSI][hapmap]
rs13207689	1.00[CEU][hapmap]
rs13212562	0.80[EUR][1000 genomes]
rs28360634	0.83[EUR][1000 genomes]
rs56114371	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56401801	0.89[EUR][1000 genomes]
rs67859638	0.81[AMR][1000 genomes]
rs71537559	0.87[EUR][1000 genomes]
rs72839445	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72839477	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7749305	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs13207082	BTN3A2	cis	Heart Left Ventricle	GTEx
rs13207082	BTN3A2	cis	multi-tissue	Pritchard
rs13207082	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs13207082	BTN3A2	cis	Esophagus Mucosa	GTEx
rs13207082	BTN3A2	cis	Nerve Tibial	GTEx
rs13207082	BTN3A2	cis	uninvolved skin	skin_eQTL
rs13207082	HLA-H	cis	multi-tissue	Pritchard
rs13207082	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs13207082	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs13207082	BTN3A2	cis	Muscle Skeletal	GTEx
rs13207082	BTN3A2	cis	Thyroid	GTEx
rs13207082	BTN3A2	cis	lung	GTEx
rs13207082	HLA-A	cis	multi-tissue	Pritchard
rs13207082	BTN3A2	cis	Artery Tibial	GTEx
rs13207082	BTN3A2	cis	Artery Aorta	GTEx
rs13207082	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs13207082	BTN3A2	cis	Whole Blood	GTEx
rs13207082	BTN3A2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27248600-27255800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:27249400-27255200	Weak transcription	HMEC	breast
3	chr6:27249400-27255600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:27250600-27252000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr6:27250600-27252200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:27250600-27252200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:27250800-27251800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:27250800-27252600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:27251000-27251400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:27251000-27252400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
11	chr6:27251200-27251400	Bivalent/Poised TSS	NHEK	skin
12	chr6:27251200-27251600	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--

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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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