Variant report

Variant	rs892289
Chromosome Location	chr12:20961322-20961323
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	FOXA2	chr12:20961309-20962079	HepG2	liver:	n/a	n/a
2	FOXA1	chr12:20961321-20961979	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SLCO1B3	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10743397	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs10770742	0.96[CEU][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs10770743	0.92[EUR][1000 genomes]
rs10770744	0.92[EUR][1000 genomes]
rs10770747	0.81[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10770748	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10841661	0.81[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs10841662	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10841664	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10841665	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10841666	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11045526	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11045527	0.93[EUR][1000 genomes]
rs11045532	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11045534	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11045542	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11045543	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1115043	0.96[EUR][1000 genomes]
rs11513214	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11513396	0.93[EUR][1000 genomes]
rs11519058	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12826518	0.86[ASN][1000 genomes]
rs1581194	0.92[EUR][1000 genomes]
rs1850012	0.93[EUR][1000 genomes]
rs1850013	0.92[EUR][1000 genomes]
rs1850014	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2138334	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2196026	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2217695	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28811026	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4094277	0.92[EUR][1000 genomes]
rs4318024	0.91[EUR][1000 genomes]
rs4762674	0.95[EUR][1000 genomes]
rs4762675	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4762676	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs4762788	0.80[EUR][1000 genomes]
rs55845073	0.86[ASN][1000 genomes]
rs61921619	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61921621	0.81[EUR][1000 genomes]
rs7133030	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs7954258	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7962265	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7971116	0.81[EUR][1000 genomes]
rs7977191	0.83[EUR][1000 genomes]
rs7977193	0.83[EUR][1000 genomes]
rs7977213	0.96[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs9971929	0.92[EUR][1000 genomes]
rs9971933	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043890	chr12:20659151-21309993	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv541410	chr12:20659151-21309993	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1054997	chr12:20682009-21292602	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv17347	chr12:20892854-21029179	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv1051454	chr12:20893994-20999635	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1040033	chr12:20914439-21078855	Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv869995	chr12:20929531-21081863	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv2758297	chr12:20942215-21117820	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv2759882	chr12:20942215-21117820	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv427905	chr12:20942215-21117820	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv428275	chr12:20942215-21117820	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv898859	chr12:20950737-21082276	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs892289	SLCO1C1	cis	parietal	SCAN
rs892289	SLCO1B3	cis	Nerve Tibial	GTEx
rs892289	AEBP2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20957800-20962400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr12:20960800-20961800	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr12:20960800-20962400	Enhancers	Primary hematopoietic stem cells	blood
4	chr12:20961000-20961400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:20961000-20961400	Enhancers	Liver	Liver
6	chr12:20961200-20962000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:20961200-20962000	Strong transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links