Variant report

Variant	rs2490054
Chromosome Location	chr6:3867557-3867558
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10447476	0.94[EUR][1000 genomes]
rs11242887	0.87[EUR][1000 genomes]
rs11242889	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11755819	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2490034	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2490050	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490052	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490053	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496386	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9392531	0.83[AFR][1000 genomes];0.99[EUR][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	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1024414	chr6:3862744-3898734	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:3855000-3869600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:3862200-3868600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:3866000-3869600	Weak transcription	Gastric	stomach
4	chr6:3867200-3867600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:3867200-3868200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:3867200-3868200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:3867200-3868600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:3867200-3869600	Enhancers	Fetal Intestine Large	intestine
9	chr6:3867200-3869600	Enhancers	Fetal Intestine Small	intestine
10	chr6:3867200-3871400	Enhancers	Stomach Mucosa	stomach
11	chr6:3867400-3867600	Enhancers	Esophagus	oesophagus
12	chr6:3867400-3868800	Enhancers	NHEK	skin
13	chr6:3867400-3869200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	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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