Variant report

Variant	rs12197040
Chromosome Location	chr6:149386313-149386314
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149376456..149387248-chr6:149393069..149406749,44	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10457075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457839	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10457842	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10499251	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12153925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12196284	1.00[JPT][hapmap]
rs12200909	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12202158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12206419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1316376	0.84[EUR][1000 genomes]
rs13190879	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13217006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17669546	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1890610	1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1890612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1934221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1934222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1934223	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1934227	0.84[CEU][hapmap]
rs2153251	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2153252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2185250	1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs34118116	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34599887	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3949414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4313020	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4332004	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4336467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4441968	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4454159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6570921	0.84[CEU][hapmap];0.82[GIH][hapmap]
rs6570923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570932	1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6900527	1.00[JPT][hapmap]
rs6901626	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6902195	0.86[EUR][1000 genomes]
rs6902487	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6909527	1.00[JPT][hapmap]
rs6909624	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6914281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6914318	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6914925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6917010	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6924503	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6930713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6930963	0.84[CEU][hapmap]
rs6932773	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6940664	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6940915	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7762928	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7773409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7776204	1.00[JPT][hapmap]
rs9322165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390652	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs9485353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9498197	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9498199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9498201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9498202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498204	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9498205	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9498207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149354400-149400600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:149362800-149401400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:149363200-149394000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:149369000-149398800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:149371400-149396400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:149371800-149397000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:149379400-149388600	Enhancers	Fetal Thymus	thymus
8	chr6:149380400-149386600	Enhancers	GM12878-XiMat	blood
9	chr6:149380800-149387400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:149380800-149388400	Enhancers	Fetal Stomach	stomach
11	chr6:149380800-149396200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:149381000-149394800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:149381000-149395000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:149381800-149394600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:149382000-149387000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:149382200-149400000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:149382400-149387000	Weak transcription	Primary B cells from cord blood	blood
18	chr6:149382400-149396000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr6:149382600-149386600	Weak transcription	Primary T cells from cord blood	blood
20	chr6:149382600-149387000	Weak transcription	Colonic Mucosa	Colon
21	chr6:149382800-149386400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr6:149382800-149386600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr6:149382800-149387000	Weak transcription	Thymus	Thymus
24	chr6:149382800-149387200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:149382800-149387200	Weak transcription	Lung	lung
26	chr6:149382800-149387200	Weak transcription	Small Intestine	intestine
27	chr6:149382800-149401400	Weak transcription	Esophagus	oesophagus
28	chr6:149383000-149386400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr6:149383000-149386600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr6:149383000-149386800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr6:149383000-149386800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:149383000-149387000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:149383000-149387000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:149383000-149387200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr6:149383000-149389200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:149383000-149394800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:149383000-149397000	Weak transcription	Pancreas	Pancrea
38	chr6:149383200-149386600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr6:149383200-149386600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr6:149383400-149386400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr6:149383400-149386600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr6:149383400-149387000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr6:149383400-149387600	Enhancers	HepG2	liver
44	chr6:149383600-149386400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr6:149383600-149386400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr6:149383600-149387200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr6:149383800-149386600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr6:149383800-149386800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:149384000-149386400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:149384000-149386800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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