Variant report

Variant	rs6964890
Chromosome Location	chr7:25388946-25388947
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1002203	0.86[EUR][1000 genomes]
rs1015497	0.85[EUR][1000 genomes]
rs10807824	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11764103	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11769627	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11972231	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11981869	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12672062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12700616	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700617	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12700618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12700619	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12700621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12700623	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12700624	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12700625	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12700628	0.86[EUR][1000 genomes]
rs13221394	0.86[EUR][1000 genomes]
rs13310680	0.91[EUR][1000 genomes]
rs1988282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1988283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2188993	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4134095	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6461862	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6461864	0.95[EUR][1000 genomes]
rs7811651	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs929239	0.86[EUR][1000 genomes]
rs929240	0.86[EUR][1000 genomes]

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	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	nsv887846	chr7:25371700-25407621	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6964890	CDCA7L	cis	parietal	SCAN
rs6964890	CPVL	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25386200-25389600	Enhancers	Fetal Lung	lung
2	chr7:25386400-25390000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:25386600-25389600	Enhancers	Fetal Intestine Large	intestine
4	chr7:25386800-25389600	Enhancers	Fetal Intestine Small	intestine
5	chr7:25387000-25389000	Enhancers	Fetal Heart	heart
6	chr7:25388000-25389600	Enhancers	Stomach Mucosa	stomach
7	chr7:25388200-25389400	Enhancers	Small Intestine	intestine
8	chr7:25388400-25389400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:25388400-25389400	Enhancers	Duodenum Mucosa	Duodenum
10	chr7:25388400-25389600	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr7:25388600-25389400	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr7:25388600-25389400	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr7:25388600-25389600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr7:25388800-25389200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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