Variant report

Variant	rs12423277
Chromosome Location	chr12:2314319-2314320
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
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];0.88[EUR][1000 genomes];0.85[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];0.85[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];0.87[ASN][1000 genomes]
rs10848628	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs10848629	0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs10848631	0.87[ASN][1000 genomes]
rs10848632	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs10848633	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs10848634	0.82[ASN][1000 genomes]
rs10848635	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs10848636	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs10848637	0.87[ASN][1000 genomes]
rs11062145	0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs11062146	0.82[ASN][1000 genomes]
rs11062156	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs11614764	0.83[ASN][1000 genomes]
rs1860056	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098013	0.85[ASN][1000 genomes]
rs2238045	0.85[ASN][1000 genomes]
rs2238046	0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2238047	0.83[ASN][1000 genomes]
rs2238048	0.89[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2238049	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2238050	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2238052	0.86[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2238053	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2238054	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2238056	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]
rs2239018	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2239019	0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2239020	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs2239021	0.87[ASN][1000 genomes]
rs2239022	0.87[ASN][1000 genomes]
rs2239023	0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2239024	0.87[ASN][1000 genomes]
rs2239025	0.87[ASN][1000 genomes]
rs2239026	0.87[ASN][1000 genomes]
rs2239027	0.87[ASN][1000 genomes]
rs2239030	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2239033	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2283287	0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2283288	0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2283291	0.85[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3794297	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4765668	0.84[ASN][1000 genomes]
rs4765669	0.87[ASN][1000 genomes]
rs4765670	0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4765902	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs6489353	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs7133502	0.85[ASN][1000 genomes]
rs7308351	0.85[ASN][1000 genomes]
rs758171	0.81[CHB][hapmap]
rs758172	0.87[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];0.87[ASN][1000 genomes]
rs7957545	0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs882195	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv898604	chr12:2236842-2317523	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
4	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
rs12423277	TEAD4	cis	cerebellum	SCAN
rs12423277	CACNA1C	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2294000-2325200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr12:2301400-2328400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:2302000-2317000	Weak transcription	Fetal Brain Male	brain
4	chr12:2305200-2322600	Weak transcription	Spleen	Spleen
5	chr12:2307800-2314400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:2308000-2322000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:2308400-2322600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:2311600-2314800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:2312800-2323000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:2313000-2320200	Weak transcription	Aorta	Aorta
11	chr12:2313200-2315200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:2313200-2317000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:2313200-2318200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:2313200-2321800	Weak transcription	Fetal Stomach	stomach
15	chr12:2314200-2314400	Enhancers	H9 Cell Line	embryonic stem cell
16	chr12:2314200-2314600	Enhancers	Fetal Heart	heart
17	chr12:2314200-2314600	Enhancers	Right Atrium	heart
18	chr12:2314200-2314800	Enhancers	Colon Smooth Muscle	Colon
19	chr12:2314200-2315000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr12:2314200-2315200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr12:2314200-2315400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr12:2314200-2315400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:2314200-2315400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:2314200-2315400	Enhancers	Left Ventricle	heart
25	chr12:2314200-2315600	Enhancers	Stomach Smooth Muscle	stomach
26	chr12:2314200-2315800	Enhancers	Rectal Smooth Muscle	rectum
27	chr12:2314200-2325000	Enhancers	Right Ventricle	heart

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