Variant report

Variant	rs10498722
Chromosome Location	chr6:25186512-25186513
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11965121	1.00[JPT][hapmap]
rs1880274	1.00[JPT][hapmap]
rs2328869	1.00[JPT][hapmap]
rs2744253	1.00[JPT][hapmap]
rs6456661	1.00[JPT][hapmap]
rs6909365	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv462663	chr6:25156197-25234884	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv601167	chr6:25156197-25234884	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10498722	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs10498722	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25175200-25192800	Weak transcription	Aorta	Aorta
2	chr6:25176200-25192800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:25177000-25191800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:25177000-25194600	Weak transcription	Placenta	Placenta
5	chr6:25179000-25187000	Weak transcription	Spleen	Spleen
6	chr6:25179800-25192600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:25181200-25186800	Weak transcription	Osteobl	bone
8	chr6:25181200-25191600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:25182600-25186600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:25182600-25186600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:25182600-25186600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:25182600-25186600	Weak transcription	NHDF-Ad	bronchial
13	chr6:25182600-25187000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:25182600-25187200	Weak transcription	NHEK	skin
15	chr6:25182800-25186800	Weak transcription	HMEC	breast
16	chr6:25182800-25187000	Weak transcription	NHLF	lung
17	chr6:25182800-25190800	Weak transcription	Hela-S3	cervix
18	chr6:25185600-25187800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

Quick Search:

Input of quick search could be:

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

what's new

Quick links