Variant report

Variant	rs4886605
Chromosome Location	chr15:75025988-75025989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75021550..75024561-chr15:75025549..75028566,3	K562	blood:
2	chr15:75021410..75023904-chr15:75025617..75029420,4	K562	blood:
3	chr15:75018522..75021766-chr15:75024358..75026673,3	MCF-7	breast:
4	chr15:75025853..75028431-chr15:75051369..75053077,3	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10459648	1.00[CEU][hapmap];0.86[MEX][hapmap]
rs11072493	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs11072494	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs11072495	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs11072496	0.88[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap]
rs11072497	0.88[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap]
rs11072498	0.88[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap]
rs11072500	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11629749	0.88[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap]
rs11629946	0.88[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap]
rs12439113	1.00[CEU][hapmap]
rs12441932	1.00[CEU][hapmap]
rs12442097	1.00[CEU][hapmap]
rs1456432	0.85[EUR][1000 genomes]
rs2068982	1.00[CEU][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap]
rs2198843	1.00[CEU][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2415242	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs3826041	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4128436	0.92[YRI][hapmap]
rs4646421	0.83[TSI][hapmap]
rs4886601	0.89[CEU][hapmap];0.82[MEX][hapmap]
rs4887159	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs4887163	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs4887166	1.00[CEU][hapmap]
rs6495116	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs6495117	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs6495118	1.00[CEU][hapmap]
rs6495121	0.88[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7161903	0.88[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap]
rs7171838	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs7178568	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap]
rs7495708	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7497342	0.88[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap]
rs8023479	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs8026923	1.00[CEU][hapmap]
rs8027066	1.00[CEU][hapmap]
rs8028430	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs8029215	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs9635320	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs9672559	1.00[CEU][hapmap];0.84[GIH][hapmap]

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	nsv904379	chr15:74869438-75027880	Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2763106	chr15:75014464-75034186	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4886605	SEMA7A	cis	cerebellum	SCAN
rs4886605	ARIH1	cis	parietal	SCAN
rs4886605	RPLP1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75019400-75033800	Weak transcription	Right Atrium	heart
2	chr15:75023800-75041600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:75025400-75027200	Weak transcription	Lung	lung
4	chr15:75025600-75027000	Weak transcription	HepG2	liver
5	chr15:75025800-75027000	Weak transcription	Liver	Liver

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