Variant report

Variant	rs1030069
Chromosome Location	chr12:12605636-12605637
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	chr12:12603843..12606415-chr12:12711459..12714793,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1019340	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]
rs1019341	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10459098	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10743982	1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs10743985	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10772563	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10772566	0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs10772567	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs10845530	0.82[CHB][hapmap]
rs10845533	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845537	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10845539	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845540	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10845541	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845542	0.90[ASN][1000 genomes]
rs10845544	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs10845545	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845546	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845551	0.94[CHB][hapmap]
rs11054894	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11054914	0.82[EUR][1000 genomes]
rs11532310	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11561172	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11609375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11829916	0.83[ASN][1000 genomes]
rs1468876	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1544682	0.90[ASN][1000 genomes]
rs2160586	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs2193270	0.89[JPT][hapmap]
rs2216264	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2417187	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3751261	0.89[CHB][hapmap]
rs3925170	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]
rs4390432	0.95[ASN][1000 genomes]
rs4488294	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4547192	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4763825	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4763826	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4763829	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4763830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56089442	0.80[ASN][1000 genomes]
rs56701819	0.85[ASN][1000 genomes]
rs56915387	0.85[ASN][1000 genomes]
rs60253266	0.80[ASN][1000 genomes]
rs61543155	0.84[ASN][1000 genomes]
rs6488526	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7132512	0.81[CEU][hapmap];0.84[CHB][hapmap];0.80[EUR][1000 genomes]
rs7135655	0.83[JPT][hapmap]
rs7295080	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73061463	0.81[ASN][1000 genomes]
rs7309503	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]
rs7309982	0.83[JPT][hapmap]
rs7310012	0.94[JPT][hapmap];0.83[YRI][hapmap];0.81[ASN][1000 genomes]
rs7311363	0.83[ASN][1000 genomes]
rs7311364	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7312010	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7313825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7315626	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7953025	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7954752	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7961703	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7967038	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7967111	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7967230	0.83[JPT][hapmap]
rs7967466	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7969020	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7969252	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7969270	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7969849	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7969984	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs879445	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs888200	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9412	0.84[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	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

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12589800-12607200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:12590600-12614600	Weak transcription	Primary B cells from cord blood	blood
3	chr12:12594400-12618200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr12:12595200-12609200	Weak transcription	GM12878-XiMat	blood
5	chr12:12595200-12618600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:12596000-12620200	Weak transcription	HSMM	muscle
7	chr12:12596000-12629800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:12596200-12620600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:12596800-12618200	Weak transcription	Primary T cells from cord blood	blood
10	chr12:12596800-12618200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr12:12597000-12617800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:12597400-12618200	Weak transcription	Gastric	stomach
13	chr12:12597400-12629000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:12598000-12607200	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:12599000-12618600	Weak transcription	Left Ventricle	heart
16	chr12:12599600-12608600	Weak transcription	NHEK	skin
17	chr12:12600400-12609000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:12600600-12616800	Weak transcription	Fetal Stomach	stomach
19	chr12:12600800-12609000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:12600800-12610200	Weak transcription	Brain Anterior Caudate	brain
21	chr12:12601000-12607200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:12601000-12609000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:12601000-12620200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:12602200-12610600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:12602600-12610600	Weak transcription	Brain Angular Gyrus	brain
26	chr12:12602800-12610000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:12603200-12606600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:12603200-12609200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr12:12603200-12609400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:12603200-12609600	Weak transcription	Brain Substantia Nigra	brain
31	chr12:12603200-12618400	Weak transcription	Esophagus	oesophagus
32	chr12:12603400-12618600	Weak transcription	Pancreas	Pancrea
33	chr12:12603800-12607200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:12603800-12614200	Weak transcription	Aorta	Aorta
35	chr12:12603800-12639200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr12:12604000-12609400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:12604000-12628600	Weak transcription	Fetal Lung	lung
38	chr12:12604400-12607200	Weak transcription	HepG2	liver
39	chr12:12604600-12608000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:12604600-12609800	Weak transcription	Hela-S3	cervix
41	chr12:12604600-12613600	Weak transcription	Fetal Intestine Small	intestine
42	chr12:12604600-12618600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr12:12605200-12618400	Weak transcription	Liver	Liver
44	chr12:12605400-12607400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:12605400-12608000	Weak transcription	Fetal Intestine Large	intestine
46	chr12:12605600-12605800	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr12:12605600-12605800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr12:12605600-12606000	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr12:12605600-12610400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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