Variant report

Variant	rs10882686
Chromosome Location	chr10:97668427-97668428
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr10:97668196-97668554	GM12878	blood:	n/a	chr10:97668409-97668418 chr10:97668407-97668420
2	RUNX3	chr10:97668187-97668492	GM12878	blood:	n/a	n/a
3	HCFC1	chr10:97666521-97668575	Hela-S3	cervix:	n/a	n/a
4	SPI1	chr10:97668255-97668485	GM12891	blood:	n/a	chr10:97668409-97668418 chr10:97668407-97668420
5	MXI1	chr10:97666727-97668501	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
ENTPD1-AS1	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10786240	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786242	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10786245	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10786250	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs10882684	0.84[AFR][1000 genomes]
rs10882690	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11188497	0.80[JPT][hapmap]
rs11188513	0.93[GIH][hapmap]
rs11188517	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11188518	0.88[JPT][hapmap]
rs1137629	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12244559	0.82[CHB][hapmap]
rs2027200	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2153914	0.93[GIH][hapmap]
rs3181129	0.82[CHB][hapmap]
rs4254003	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4303172	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4415682	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4614366	0.82[CHB][hapmap]
rs7101331	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7904410	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs7906654	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7908420	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs7908691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7921331	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs7922217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7922992	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv895905	chr10:97513362-97686064	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv895906	chr10:97513362-97703650	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv895907	chr10:97529318-97686064	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv895908	chr10:97544513-97724247	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10882686	CYP2C19	cis	parietal	SCAN
rs10882686	ENTPD1	cis	lymphoblastoid	seeQTL
rs10882686	ENTPD1	Cis_1M	lymphoblastoid	RTeQTL
rs10882686	ZNF518A	cis	cerebellum	SCAN
rs10882686	ENTPD1	cis	multi-tissue	Pritchard
rs10882686	ENTPD1	cis	Lymphoblastoid	GTEx
rs10882686	PDE6C	cis	cerebellum	SCAN
rs10882686	ALDH18A1	cis	cerebellum	SCAN
rs10882686	TCTN3	cis	lymphoblastoid	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97668000-97668600	Flanking Active TSS	GM12878-XiMat	blood
2	chr10:97668000-97670000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:97668000-97670400	Weak transcription	Pancreas	Pancrea
4	chr10:97668200-97670800	Weak transcription	Right Atrium	heart
5	chr10:97668200-97693600	Weak transcription	Fetal Stomach	stomach
6	chr10:97668400-97669000	Enhancers	HepG2	liver
7	chr10:97668400-97673600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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