Variant report

Variant	rs6719619
Chromosome Location	chr2:173511917-173511918
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11890332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11892961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11896816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11899916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11902846	1.00[AMR][1000 genomes]
rs11902922	1.00[AMR][1000 genomes]
rs35846102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58799457	1.00[AMR][1000 genomes]
rs7567024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7592130	1.00[AFR][1000 genomes];1.00[AMR][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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv583665	chr2:173460640-173643087	Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv2762962	chr2:173493078-173527311	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6719619	TRAT1	trans	lymphoblastoid	seeQTL
rs6719619	CXCL14	trans	lymphoblastoid	seeQTL
rs6719619	SCRN1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173499800-173513000	Weak transcription	Pancreas	Pancrea
2	chr2:173505000-173512000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:173505400-173512000	Weak transcription	HSMM	muscle
4	chr2:173508600-173512000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:173508800-173512000	Weak transcription	NHEK	skin
6	chr2:173509200-173519400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:173511200-173512800	Enhancers	NHDF-Ad	bronchial
8	chr2:173511200-173513400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:173511600-173512800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr2:173511800-173512000	Bivalent Enhancer	Small Intestine	intestine
11	chr2:173511800-173512200	Enhancers	Osteobl	bone
12	chr2:173511800-173512600	Enhancers	HMEC	breast
13	chr2:173511800-173512800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:173511800-173512800	Enhancers	NH-A	brain
15	chr2:173511800-173513000	Enhancers	HUVEC	blood vessel
16	chr2:173511800-173513000	Enhancers	NHLF	lung
17	chr2:173511800-173513600	Enhancers	Foreskin Fibroblast Primary Cells skin01	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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