Variant report

Variant	rs28609543
Chromosome Location	chr7:25357890-25357891
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:9)

rs_ID	r²[population]
rs10239108	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10249367	0.80[AFR][1000 genomes]
rs10260041	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10270076	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13438356	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57576520	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61545837	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975649	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7802048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv606424	chr7:24982529-25466521	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv606426	chr7:25254125-25621579	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1028018	chr7:25351950-25371700	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
4	nsv464409	chr7:25352809-25371700	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
5	nsv464410	chr7:25354077-25371700	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
6	nsv606427	chr7:25354077-25371700	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25351000-25358400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:25351600-25358200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:25353800-25358400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr7:25354000-25360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:25355000-25360000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:25355200-25358200	Weak transcription	Ovary	ovary
7	chr7:25355200-25358600	Weak transcription	Liver	Liver
8	chr7:25355400-25361000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr7:25356200-25360000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr7:25356200-25360800	Weak transcription	Fetal Intestine Large	intestine
11	chr7:25356400-25361000	Weak transcription	Fetal Lung	lung
12	chr7:25357200-25358000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr7:25357200-25358400	Weak transcription	Fetal Intestine Small	intestine
14	chr7:25357600-25360000	Weak transcription	Pancreas	Pancrea
15	chr7:25357800-25358600	Enhancers	Brain Anterior Caudate	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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