Variant report

Variant	rs4762779
Chromosome Location	chr12:20920880-20920881
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10505869	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10841614	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10841617	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10841619	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10841621	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10841627	0.85[EUR][1000 genomes]
rs10841642	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10841644	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10841645	0.87[EUR][1000 genomes]
rs10841648	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11045455	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045458	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11045459	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11045460	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11045477	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11045500	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11045505	0.87[EUR][1000 genomes]
rs11519245	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11525531	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12313384	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12371798	0.83[JPT][hapmap]
rs12823467	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1588918	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1588919	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1588920	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1829008	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037154	0.83[EUR][1000 genomes]
rs2090272	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2090274	0.98[EUR][1000 genomes]
rs2090275	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2090276	0.98[EUR][1000 genomes]
rs2102737	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2417859	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2900456	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35811140	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4141475	0.87[EUR][1000 genomes]
rs4340099	0.84[EUR][1000 genomes]
rs4379890	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4762776	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4762778	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4762780	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4762781	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4762785	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4762786	0.87[EUR][1000 genomes]
rs6487139	0.88[EUR][1000 genomes]
rs6487140	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7294687	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7295794	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7297868	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7299977	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7300887	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309696	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7311295	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7315732	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7964850	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7965380	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7968058	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7980075	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs953002	0.80[MEX][hapmap]
rs9795878	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1039951	chr12:20880417-20941238	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	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
6	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
7	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4762779	SLCO1C1	cis	cerebellum	SCAN
rs4762779	SLCO1C1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20892800-20922200	Weak transcription	Aorta	Aorta
2	chr12:20917000-20922200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:20917400-20921800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:20919200-20922200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:20920600-20921000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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