Variant report

Variant	rs1019340
Chromosome Location	chr12:12586936-12586937
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12567548..12570120-chr12:12585804..12588751,2	K562	blood:
2	chr12:12586017..12588316-chr12:12590751..12594080,4	MCF-7	breast:
3	chr12:12583532..12588192-chr12:12712241..12716569,6	MCF-7	breast:
4	chr12:12555144..12557679-chr12:12584651..12587421,2	MCF-7	breast:
5	chr12:12585154..12587751-chr12:12741127..12742716,2	MCF-7	breast:
6	chr12:12586894..12590134-chr12:12591817..12594282,3	K562	blood:
7	chr12:12578734..12582406-chr12:12583548..12588483,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1019341	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1030069	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10459098	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743982	1.00[ASW][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10743985	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772563	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772566	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10772567	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10845530	0.88[CHB][hapmap]
rs10845533	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845537	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845539	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845540	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10845541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845542	0.91[ASN][1000 genomes]
rs10845544	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10845545	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845546	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845551	0.89[CHB][hapmap]
rs11054894	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11054914	0.81[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs11532310	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11561172	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11609375	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11829916	0.85[ASN][1000 genomes]
rs1468876	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1544682	0.91[ASN][1000 genomes]
rs2160586	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[ASN][1000 genomes]
rs2193269	0.82[ASN][1000 genomes]
rs2193270	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2216264	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2417187	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28853875	0.82[ASN][1000 genomes]
rs35908046	0.83[EUR][1000 genomes]
rs3751261	0.83[CHB][hapmap]
rs3925170	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4390432	0.97[ASN][1000 genomes]
rs4488294	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4547192	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763825	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763826	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763829	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4763830	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56089442	0.82[ASN][1000 genomes]
rs56701819	0.87[ASN][1000 genomes]
rs56796062	0.81[ASN][1000 genomes]
rs56915387	0.87[ASN][1000 genomes]
rs60253266	0.82[ASN][1000 genomes]
rs61543155	0.86[ASN][1000 genomes]
rs6488525	0.83[AFR][1000 genomes]
rs6488526	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132512	0.80[GIH][hapmap];0.89[TSI][hapmap]
rs7135655	0.84[JPT][hapmap]
rs7295080	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7300150	0.81[ASN][1000 genomes]
rs73061463	0.83[ASN][1000 genomes]
rs7309503	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]
rs7309982	0.84[JPT][hapmap]
rs7310012	1.00[ASW][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7311363	0.86[ASN][1000 genomes]
rs7311364	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7312010	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7313825	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7315626	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7953025	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]
rs7954752	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961703	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7967038	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7967111	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7967230	0.84[JPT][hapmap];0.88[MEX][hapmap]
rs7967466	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7969020	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7969252	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969270	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7969849	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969984	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879445	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs888200	0.93[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9645752	0.81[CHB][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1019340	ETV6	cis	cerebellum	SCAN
rs1019340	ATF7IP	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12572600-12588400	Weak transcription	Primary T cells from cord blood	blood
2	chr12:12578200-12588600	Weak transcription	Primary B cells from cord blood	blood
3	chr12:12578400-12588200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr12:12578800-12589200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:12579400-12587000	Weak transcription	Psoas Muscle	Psoas
6	chr12:12580000-12588600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:12580800-12587400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:12581200-12587000	Enhancers	NHEK	skin
9	chr12:12581600-12588800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr12:12582000-12589200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:12582600-12592000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr12:12582600-12595000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:12582600-12599400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:12582800-12592600	Weak transcription	NH-A	brain
15	chr12:12582800-12596400	Weak transcription	Spleen	Spleen
16	chr12:12583000-12588600	Weak transcription	GM12878-XiMat	blood
17	chr12:12583000-12589400	Weak transcription	HSMM	muscle
18	chr12:12583000-12594000	Weak transcription	HSMMtube	muscle
19	chr12:12583400-12587400	Enhancers	NHLF	lung
20	chr12:12583600-12588000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:12583800-12587400	Enhancers	Fetal Stomach	stomach
22	chr12:12584000-12587400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:12584000-12588000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:12584000-12598600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:12584200-12588200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr12:12584200-12588600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:12584200-12588600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr12:12584200-12589200	Enhancers	Fetal Lung	lung
29	chr12:12584200-12590200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:12584200-12592200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr12:12584200-12592800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:12584200-12593200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:12584400-12592000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr12:12584800-12587200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:12584800-12587600	Enhancers	A549	lung
36	chr12:12584800-12588400	Enhancers	Brain Substantia Nigra	brain
37	chr12:12585000-12587400	Enhancers	NHDF-Ad	bronchial
38	chr12:12585200-12587000	Enhancers	Stomach Mucosa	stomach
39	chr12:12585200-12587400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:12585200-12587400	Enhancers	Stomach Smooth Muscle	stomach
41	chr12:12585200-12588400	Enhancers	HepG2	liver
42	chr12:12585400-12587400	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr12:12585400-12588400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr12:12585400-12588400	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr12:12585400-12593200	Weak transcription	Small Intestine	intestine
46	chr12:12585600-12587200	Enhancers	Brain Angular Gyrus	brain
47	chr12:12585600-12587400	Enhancers	Brain Anterior Caudate	brain
48	chr12:12585600-12589200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr12:12585600-12590200	Weak transcription	HMEC	breast
50	chr12:12585600-12592000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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