Variant report

Variant	rs7135015
Chromosome Location	chr12:105296956-105296957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1002803	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap]
rs10507184	0.86[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs10746008	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10778355	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10778358	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10861294	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10861296	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11112253	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1155994	0.85[ASN][1000 genomes]
rs1389612	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1565813	0.86[ASW][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap]
rs2131806	0.80[GIH][hapmap]
rs2248012	0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2248986	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2249454	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2264892	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2453155	0.83[GIH][hapmap]
rs2453156	0.95[CHB][hapmap]
rs2453160	0.83[ASN][1000 genomes]
rs2453161	0.86[CHD][hapmap]
rs2453166	0.86[ASW][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2463018	0.95[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap]
rs2463439	0.85[CHB][hapmap]
rs2463440	0.85[CHB][hapmap];0.88[CHD][hapmap]
rs2463441	0.86[CHD][hapmap]
rs2468089	0.82[GIH][hapmap]
rs2468092	0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2468099	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs2468100	0.85[ASN][1000 genomes]
rs2468105	0.95[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2468109	0.86[CHD][hapmap]
rs2468337	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2468340	0.85[ASN][1000 genomes]
rs2730291	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap]
rs4076550	0.86[CEU][hapmap]
rs4334113	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4388976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4393404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4964310	0.87[JPT][hapmap]
rs6539170	0.86[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs6539171	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs703681	0.88[CHD][hapmap]
rs7138686	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7309240	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73193606	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7967503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7968763	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7980681	0.84[ASN][1000 genomes]
rs9668618	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs996294	0.87[CEU][hapmap]

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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7135015	C12orf23	cis	parietal	SCAN
rs7135015	C12orf42	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105275400-105297000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:105278600-105313800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:105284600-105309000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:105290600-105297200	Weak transcription	HepG2	liver
5	chr12:105290800-105331600	Weak transcription	Gastric	stomach
6	chr12:105292000-105297600	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:105293400-105302600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:105293400-105310000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:105293600-105303800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:105293600-105321600	Weak transcription	A549	lung
11	chr12:105294400-105297200	Enhancers	Liver	Liver
12	chr12:105295600-105297200	Enhancers	Stomach Mucosa	stomach
13	chr12:105296200-105297200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:105296400-105298600	Enhancers	Pancreas	Pancrea
15	chr12:105296800-105297200	Enhancers	Aorta	Aorta

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