Variant report

Variant	rs10744560
Chromosome Location	chr12:2387099-2387100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1006737	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1024582	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10774034	0.82[JPT][hapmap]
rs10774035	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10774036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10774037	0.81[MEX][hapmap]
rs11062170	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12311439	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12315711	0.96[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12424245	1.00[JPT][hapmap]
rs2159100	0.96[CEU][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4298967	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4765904	0.82[JPT][hapmap]
rs4765905	0.96[CEU][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4765914	0.81[MEX][hapmap]
rs7297582	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs758170	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs769087	0.96[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7965923	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10744560	CACNA1C	cis	cerebellum	SCAN
rs10744560	SLC6A12	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2374400-2393800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:2378000-2397600	Weak transcription	Lung	lung
3	chr12:2378200-2393000	Weak transcription	Colonic Mucosa	Colon
4	chr12:2379800-2391400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:2381200-2387200	Enhancers	Right Ventricle	heart
6	chr12:2381200-2388600	Enhancers	Fetal Heart	heart
7	chr12:2382000-2393000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:2383200-2391400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:2383400-2391400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:2383400-2391800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:2383400-2392400	Weak transcription	Aorta	Aorta
12	chr12:2383400-2393000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:2383600-2391200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:2383600-2391400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:2383600-2392800	Weak transcription	Right Atrium	heart
16	chr12:2386000-2387200	Enhancers	Left Ventricle	heart
17	chr12:2386000-2390600	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:2386200-2391400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:2386200-2392600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:2386800-2387400	Enhancers	NHDF-Ad	bronchial

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