Variant report

Variant	rs7309503
Chromosome Location	chr12:12600701-12600702
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	chr12:12594582..12598614-chr12:12600481..12604032,6	MCF-7	breast:
2	chr12:12598434..12601352-chr12:12712226..12715206,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1019340	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1019341	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1030069	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10459098	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743982	0.93[ASW][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs10743985	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772563	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772566	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs10772567	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs10845530	0.88[CHB][hapmap]
rs10845533	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845537	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10845539	0.87[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845540	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10845541	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845542	0.92[ASN][1000 genomes]
rs10845544	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs10845545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845546	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845551	0.89[CHB][hapmap]
rs11054894	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11054914	0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs11532310	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11561172	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11609375	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11829916	0.85[ASN][1000 genomes]
rs1468876	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544682	0.92[ASN][1000 genomes]
rs16908059	0.81[CHD][hapmap]
rs16908062	0.81[CHD][hapmap]
rs16908076	0.81[CHD][hapmap]
rs16908101	0.81[CHD][hapmap]
rs2160586	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[ASN][1000 genomes]
rs2193269	0.81[ASN][1000 genomes]
rs2193270	0.81[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2216264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2417187	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28853875	0.81[ASN][1000 genomes]
rs3751261	0.83[CHB][hapmap]
rs3925170	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4390432	0.97[ASN][1000 genomes]
rs4488294	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4547192	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4763825	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4763826	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4763829	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763830	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56089442	0.82[ASN][1000 genomes]
rs56701819	0.86[ASN][1000 genomes]
rs56796062	0.81[ASN][1000 genomes]
rs56915387	0.86[ASN][1000 genomes]
rs60253266	0.82[ASN][1000 genomes]
rs61543155	0.86[ASN][1000 genomes]
rs6488526	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7132512	0.80[CEU][hapmap];0.89[TSI][hapmap]
rs7135655	0.84[JPT][hapmap]
rs7295080	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7300150	0.80[ASN][1000 genomes]
rs73061463	0.82[ASN][1000 genomes]
rs7309982	0.84[JPT][hapmap]
rs7310012	0.93[ASW][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs7311363	0.85[ASN][1000 genomes]
rs7311364	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312010	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7313825	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7315626	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953025	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]
rs7954752	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7961703	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7967038	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967111	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7967230	0.82[ASW][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs7967466	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7969020	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7969252	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7969270	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7969849	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7969984	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs879445	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888200	0.87[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9645752	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	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	nsv898810	chr12:12600080-12627410	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3342500	chr12:12600571-12600886	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7309503	ETV6	cis	cerebellum	SCAN
rs7309503	ATF7IP	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12589800-12607200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:12590400-12601800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:12590600-12614600	Weak transcription	Primary B cells from cord blood	blood
4	chr12:12592200-12602200	Enhancers	Fetal Thymus	thymus
5	chr12:12594400-12618200	Weak transcription	Primary B cells from peripheral blood	blood
6	chr12:12595000-12602200	Weak transcription	Placenta	Placenta
7	chr12:12595200-12602800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:12595200-12609200	Weak transcription	GM12878-XiMat	blood
9	chr12:12595200-12618600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:12596000-12602200	Weak transcription	A549	lung
11	chr12:12596000-12620200	Weak transcription	HSMM	muscle
12	chr12:12596000-12629800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:12596200-12620600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:12596400-12603200	Weak transcription	Aorta	Aorta
15	chr12:12596600-12601000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:12596800-12602000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:12596800-12602400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr12:12596800-12603000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:12596800-12604600	Weak transcription	NHLF	lung
20	chr12:12596800-12618200	Weak transcription	Primary T cells from cord blood	blood
21	chr12:12596800-12618200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:12597000-12601600	Weak transcription	Spleen	Spleen
23	chr12:12597000-12602400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:12597000-12602600	Weak transcription	Esophagus	oesophagus
25	chr12:12597000-12603000	Weak transcription	Psoas Muscle	Psoas
26	chr12:12597000-12617800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:12597200-12603000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr12:12597400-12601600	Weak transcription	Pancreas	Pancrea
29	chr12:12597400-12601800	Weak transcription	Liver	Liver
30	chr12:12597400-12618200	Weak transcription	Gastric	stomach
31	chr12:12597400-12629000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr12:12597600-12602000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr12:12598000-12602200	Enhancers	HepG2	liver
34	chr12:12598000-12607200	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:12598200-12602000	Weak transcription	Small Intestine	intestine
36	chr12:12598200-12602000	Weak transcription	Stomach Mucosa	stomach
37	chr12:12599000-12618600	Weak transcription	Left Ventricle	heart
38	chr12:12599200-12601000	Enhancers	Fetal Lung	lung
39	chr12:12599200-12601200	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr12:12599200-12601800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:12599400-12601200	Enhancers	Thymus	Thymus
42	chr12:12599400-12602200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:12599600-12600800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:12599600-12600800	Enhancers	Brain Cingulate Gyrus	brain
45	chr12:12599600-12600800	Enhancers	Brain Substantia Nigra	brain
46	chr12:12599600-12601000	Enhancers	Adipose Nuclei	Adipose
47	chr12:12599600-12608600	Weak transcription	NHEK	skin
48	chr12:12599800-12600800	Enhancers	Brain Anterior Caudate	brain
49	chr12:12599800-12600800	Enhancers	Right Ventricle	heart
50	chr12:12599800-12601000	Enhancers	Primary T helper cells PMA-I stimulated	--

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