Variant report

Variant	rs2238056
Chromosome Location	chr12:2327944-2327945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1016388	0.81[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10459125	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10744559	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs10774030	0.81[CHB][hapmap]
rs10774032	0.86[ASN][1000 genomes]
rs10774033	0.94[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs10848627	0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10848628	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10848629	0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10848631	0.86[ASN][1000 genomes]
rs10848632	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10848633	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10848634	0.82[ASN][1000 genomes]
rs10848635	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10848636	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10848637	0.86[ASN][1000 genomes]
rs11062145	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs11062146	0.81[ASN][1000 genomes]
rs11062156	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs11614764	0.82[ASN][1000 genomes]
rs12423277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1860056	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2098013	0.85[ASN][1000 genomes]
rs2238045	0.84[ASN][1000 genomes]
rs2238046	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2238047	0.83[ASN][1000 genomes]
rs2238048	0.89[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2238049	0.81[JPT][hapmap]
rs2238050	0.81[JPT][hapmap]
rs2238052	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs2238053	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2238054	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2239018	0.81[JPT][hapmap]
rs2239019	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2239020	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs2239021	0.86[ASN][1000 genomes]
rs2239022	0.86[ASN][1000 genomes]
rs2239023	0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2239024	0.86[ASN][1000 genomes]
rs2239025	0.86[ASN][1000 genomes]
rs2239026	0.86[ASN][1000 genomes]
rs2239027	0.86[ASN][1000 genomes]
rs2239030	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2239033	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2283287	0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2283288	0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2283291	0.85[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3794297	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4765668	0.84[ASN][1000 genomes]
rs4765669	0.86[ASN][1000 genomes]
rs4765670	0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4765902	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs6489353	0.95[CHB][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7133502	0.84[ASN][1000 genomes]
rs7308351	0.84[ASN][1000 genomes]
rs758171	0.81[CHB][hapmap]
rs758172	0.86[ASN][1000 genomes]
rs758173	0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs758174	0.94[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs7957545	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs882195	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv898605	chr12:2252924-2327944	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2238056	TEAD4	cis	cerebellum	SCAN
rs2238056	CACNA1C	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2301400-2328400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:2320400-2335800	Weak transcription	NHLF	lung
3	chr12:2320600-2328000	Weak transcription	Aorta	Aorta
4	chr12:2320800-2331400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:2323200-2340200	Enhancers	Fetal Heart	heart
6	chr12:2323400-2328200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:2323600-2336000	Weak transcription	Fetal Muscle Leg	muscle
8	chr12:2323800-2338800	Weak transcription	Spleen	Spleen
9	chr12:2325400-2328600	Weak transcription	Fetal Stomach	stomach
10	chr12:2325400-2329800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:2325400-2330400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:2325800-2334600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:2326000-2334600	Weak transcription	Osteobl	bone
14	chr12:2326600-2328600	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr12:2326600-2330800	Enhancers	Left Ventricle	heart
16	chr12:2327200-2328800	Enhancers	Fetal Lung	lung
17	chr12:2327200-2329800	Enhancers	Right Atrium	heart
18	chr12:2327200-2336200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:2327600-2328000	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:2327600-2328400	Weak transcription	Right Ventricle	heart
21	chr12:2327600-2329200	Weak transcription	Rectal Smooth Muscle	rectum

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