Variant report

Variant	rs7964129
Chromosome Location	chr12:40161249-40161250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40158968..40161311-chr12:40166240..40167816,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10047563	0.81[AMR][1000 genomes]
rs10219652	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10444570	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10735885	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10747853	0.82[AMR][1000 genomes]
rs10747877	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747878	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783994	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10783998	0.81[AMR][1000 genomes]
rs10784016	0.81[AMR][1000 genomes]
rs10784034	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10784051	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10784059	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877335	0.81[AMR][1000 genomes]
rs10877337	0.81[AMR][1000 genomes]
rs10877410	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11173259	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11173260	0.81[AMR][1000 genomes]
rs11173376	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11173394	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173401	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173411	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173423	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173424	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173428	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173433	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173434	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173440	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173446	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173459	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173494	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173507	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11173541	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173550	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173551	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11173553	0.92[ASN][1000 genomes]
rs11532458	0.92[ASN][1000 genomes]
rs12229203	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12229418	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12230687	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12299938	0.84[ASN][1000 genomes]
rs12823801	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4238072	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4238073	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4255599	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4255600	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4312128	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4322460	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4322461	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4381428	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4388963	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4391875	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4397916	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4405390	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4405391	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4411336	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4417381	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4556618	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4767949	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4768169	0.81[AMR][1000 genomes]
rs4768170	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57244766	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58418587	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61931185	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61931208	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61931211	0.86[ASN][1000 genomes]
rs61933102	0.81[AMR][1000 genomes]
rs61933154	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61933157	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61933158	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6421195	0.81[AMR][1000 genomes]
rs6421196	0.81[AMR][1000 genomes]
rs6421197	0.81[AMR][1000 genomes]
rs6581263	0.81[AMR][1000 genomes]
rs6581270	0.81[AMR][1000 genomes]
rs6581271	0.81[AMR][1000 genomes]
rs6581294	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7136929	0.81[AMR][1000 genomes]
rs7296585	0.81[AMR][1000 genomes]
rs7298453	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7301886	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7302849	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7308955	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7485345	0.81[AMR][1000 genomes]
rs7486621	0.81[AMR][1000 genomes]
rs7952735	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7956577	0.81[AMR][1000 genomes]
rs7959905	0.81[AMR][1000 genomes]
rs7969282	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1037457	chr12:39898349-40245401	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv541480	chr12:39898349-40245401	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv899024	chr12:40046408-40188870	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1053603	chr12:40082673-40197609	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv427907	chr12:40122713-40199621	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv428280	chr12:40122713-40199621	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40144800-40166400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr12:40145000-40175000	Weak transcription	Right Ventricle	heart
3	chr12:40146000-40166800	Weak transcription	Ovary	ovary
4	chr12:40153200-40171400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:40156400-40172800	Weak transcription	Fetal Intestine Small	intestine
6	chr12:40158000-40163600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:40158000-40173600	Weak transcription	Aorta	Aorta
8	chr12:40158200-40161400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:40158200-40166400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:40158200-40166400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:40158200-40174400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:40158200-40179000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:40158200-40199000	Weak transcription	Left Ventricle	heart
14	chr12:40160600-40161400	Enhancers	NHDF-Ad	bronchial
15	chr12:40160600-40165000	Weak transcription	Hela-S3	cervix
16	chr12:40161000-40166600	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:40161200-40161600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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