Variant report

Variant	rs4141475
Chromosome Location	chr12:20951861-20951862
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:20639028..20639571-chr12:20951385..20952022,2	MCF-7	breast:
2	chr12:20798899..20799416-chr12:20951641..20952181,2	MCF-7	breast:
3	chr12:20798864..20799798-chr12:20951213..20952118,4	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10505869	0.86[EUR][1000 genomes]
rs10841614	0.84[EUR][1000 genomes]
rs10841617	0.86[EUR][1000 genomes]
rs10841642	0.99[EUR][1000 genomes]
rs10841644	0.99[EUR][1000 genomes]
rs10841645	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10841648	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11045455	0.86[EUR][1000 genomes]
rs11045458	0.86[EUR][1000 genomes]
rs11045459	0.88[EUR][1000 genomes]
rs11045460	0.86[EUR][1000 genomes]
rs11045477	0.90[EUR][1000 genomes]
rs11045500	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11045505	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11525531	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12313384	0.99[EUR][1000 genomes]
rs12823467	0.99[EUR][1000 genomes]
rs1588918	0.90[EUR][1000 genomes]
rs1588919	0.90[EUR][1000 genomes]
rs1588920	0.91[EUR][1000 genomes]
rs1829008	0.98[EUR][1000 genomes]
rs2037154	0.82[ASN][1000 genomes]
rs2090272	0.86[EUR][1000 genomes]
rs2090274	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2090275	0.85[EUR][1000 genomes]
rs2090276	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2102737	0.86[EUR][1000 genomes]
rs2417859	0.86[EUR][1000 genomes]
rs2900456	0.85[EUR][1000 genomes]
rs35811140	0.99[EUR][1000 genomes]
rs4762776	0.85[EUR][1000 genomes]
rs4762779	0.87[EUR][1000 genomes]
rs4762780	0.90[EUR][1000 genomes]
rs4762781	0.90[EUR][1000 genomes]
rs4762785	0.99[EUR][1000 genomes]
rs4762786	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487140	0.83[EUR][1000 genomes]
rs7294687	0.99[EUR][1000 genomes]
rs7295794	0.84[EUR][1000 genomes]
rs7297868	0.82[EUR][1000 genomes]
rs7299977	0.85[EUR][1000 genomes]
rs7300887	0.89[EUR][1000 genomes]
rs7309696	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311295	0.90[EUR][1000 genomes]
rs7315732	0.87[EUR][1000 genomes]
rs7964850	0.86[EUR][1000 genomes]
rs7965380	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7968058	0.86[EUR][1000 genomes]
rs7980075	0.93[AFR][1000 genomes];0.99[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4141475	SLCO1C1	cis	parietal	SCAN
rs4141475	SLCO1C1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20942600-20961200	Weak transcription	A549	lung
2	chr12:20951200-20952000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:20951200-20953000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:20951600-20952800	Weak transcription	Adipose Nuclei	Adipose
5	chr12:20951600-20953200	Weak transcription	Liver	Liver
6	chr12:20951800-20952200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links