Variant report

Variant	rs6962233
Chromosome Location	chr7:140797570-140797571
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:140774135..140775705-chr7:140796756..140798922,2	MCF-7	breast:
2	chr7:140790828..140792569-chr7:140797247..140798946,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261115	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11762357	0.92[ASN][1000 genomes]
rs1860752	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2365575	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4726263	0.94[ASN][1000 genomes]
rs491554	0.94[ASN][1000 genomes]
rs498933	0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs511001	0.94[ASN][1000 genomes]
rs534348	0.94[ASN][1000 genomes]
rs536809	0.91[ASN][1000 genomes]
rs553046	0.94[ASN][1000 genomes]
rs55949610	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs560981	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6464278	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs6464330	0.82[ASW][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6944492	0.94[ASN][1000 genomes]
rs6960603	0.89[ASN][1000 genomes]
rs6967482	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs722219	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7778658	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7805034	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806026	0.94[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7810146	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs801157	0.94[ASN][1000 genomes]
rs801158	0.94[ASN][1000 genomes]
rs9640323	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889248	chr7:140754785-140809205	Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3336433	chr7:140783089-140892541	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6962233	TRPV5	cis	cerebellum	SCAN
rs6962233	RAB19	cis	parietal	SCAN
rs6962233	ADCK2	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140783400-140800600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:140783400-140801400	Weak transcription	Fetal Brain Male	brain
3	chr7:140794400-140801200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:140794400-140801400	Weak transcription	Brain Germinal Matrix	brain
5	chr7:140795000-140801600	Weak transcription	Fetal Brain Female	brain
6	chr7:140796000-140802400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:140796000-140803800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr7:140796200-140803600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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