Variant report

Variant	rs7953025
Chromosome Location	chr12:12557507-12557508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12557174..12559424-chr12:12713133..12714808,2	MCF-7	breast:
2	chr12:12550258..12553161-chr12:12554299..12558157,3	MCF-7	breast:
3	chr12:12555144..12557679-chr12:12584651..12587421,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1019340	0.93[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1019341	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1030069	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10459098	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10743982	0.93[ASW][hapmap];0.92[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10743983	0.84[ASN][1000 genomes]
rs10743985	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10772563	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10772566	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10772567	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10845530	0.88[CHB][hapmap]
rs10845533	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10845537	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10845539	0.87[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10845540	0.85[ASN][1000 genomes]
rs10845541	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10845542	0.85[ASN][1000 genomes]
rs10845544	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10845545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10845546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10845551	0.89[CHB][hapmap]
rs11054894	0.89[ASN][1000 genomes]
rs11532310	0.89[ASN][1000 genomes]
rs11561172	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11609375	0.81[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1468876	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1544682	0.85[ASN][1000 genomes]
rs2160586	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[ASN][1000 genomes]
rs2193269	0.86[ASN][1000 genomes]
rs2193270	0.82[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2216264	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2417187	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28853875	0.86[ASN][1000 genomes]
rs3751261	0.83[CHB][hapmap]
rs3925170	0.93[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4390432	0.91[ASN][1000 genomes]
rs4488294	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4547192	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4763825	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4763826	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4763829	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4763830	0.81[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56089442	0.85[ASN][1000 genomes]
rs56701819	0.81[ASN][1000 genomes]
rs56796062	0.86[ASN][1000 genomes]
rs56915387	0.81[ASN][1000 genomes]
rs57348917	0.86[ASN][1000 genomes]
rs6488526	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7132512	0.80[GIH][hapmap]
rs7135655	0.84[JPT][hapmap]
rs7295080	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300150	0.87[ASN][1000 genomes]
rs73061463	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7309503	0.87[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7309982	0.84[JPT][hapmap]
rs7310012	0.93[ASW][hapmap];0.96[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7311363	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7311364	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7313825	0.81[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7315626	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73283441	0.81[ASN][1000 genomes]
rs7954752	0.93[ASN][1000 genomes]
rs7961703	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7967038	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7967111	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs7967230	0.84[JPT][hapmap];0.96[MEX][hapmap]
rs7967466	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969020	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7969252	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7969270	0.92[ASN][1000 genomes]
rs7969849	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7969984	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs879445	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs888200	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9645752	0.80[CHB][hapmap];0.82[CHD][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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7953025	ETV6	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12526400-12558800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:12535400-12561400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr12:12537200-12576000	Weak transcription	Primary B cells from cord blood	blood
4	chr12:12538600-12561800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:12540200-12560600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:12541400-12562800	Weak transcription	Psoas Muscle	Psoas
7	chr12:12543000-12558800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:12551000-12559000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:12551200-12558800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:12551600-12558800	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:12552000-12557800	Weak transcription	Gastric	stomach
12	chr12:12552000-12558800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:12552000-12558800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:12552000-12558800	Weak transcription	Lung	lung
15	chr12:12552000-12559000	Weak transcription	HSMM	muscle
16	chr12:12552000-12559800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:12552000-12561400	Weak transcription	HSMMtube	muscle
18	chr12:12552000-12569000	Weak transcription	Hela-S3	cervix
19	chr12:12552200-12558600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:12552800-12558600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr12:12552800-12558800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:12553200-12561400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:12553400-12558000	Weak transcription	Brain Angular Gyrus	brain
24	chr12:12553400-12558400	Weak transcription	Brain Anterior Caudate	brain
25	chr12:12553400-12558600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:12553400-12558800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:12553400-12558800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:12553400-12559000	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:12554200-12558600	Weak transcription	GM12878-XiMat	blood
30	chr12:12555000-12560600	Enhancers	Fetal Intestine Large	intestine
31	chr12:12555200-12558000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr12:12555200-12559200	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr12:12555200-12560200	Enhancers	Fetal Intestine Small	intestine
34	chr12:12555200-12560800	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr12:12555400-12557600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:12555400-12559200	Enhancers	Placenta	Placenta
37	chr12:12555600-12558600	Weak transcription	Aorta	Aorta
38	chr12:12556000-12557600	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr12:12556000-12557600	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr12:12556000-12557600	Enhancers	Fetal Thymus	thymus
41	chr12:12556000-12559000	Enhancers	Brain Substantia Nigra	brain
42	chr12:12556000-12560000	Enhancers	Liver	Liver
43	chr12:12556000-12560200	Enhancers	Stomach Mucosa	stomach
44	chr12:12556200-12557600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr12:12556200-12557600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:12556200-12557600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:12556200-12558000	Enhancers	Pancreas	Pancrea
48	chr12:12556200-12558000	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr12:12556200-12558800	Enhancers	Brain Hippocampus Middle	brain
50	chr12:12556200-12560200	Enhancers	Brain Cingulate Gyrus	brain

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