Variant report

Variant	rs12776460
Chromosome Location	chr10:50288931-50288932
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50287416..50289075-chr10:50291865..50294530,2	MCF-7	breast:
2	chr10:50288196..50290467-chr10:50297375..50300354,2	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs12244666	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12244748	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12253426	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12255090	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12256777	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12257242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12269023	0.80[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap]
rs12765281	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs12769361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12774293	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17011744	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17011746	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17011757	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17700872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17701186	0.88[EUR][1000 genomes]
rs17773851	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs2003044	0.95[CEU][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs2137911	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2137912	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2137914	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2246463	0.94[CHB][hapmap];0.97[CHD][hapmap]
rs2246673	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2246937	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2264846	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2264847	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2490838	0.85[EUR][1000 genomes]
rs2725179	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2725181	0.95[CEU][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs2725184	0.86[EUR][1000 genomes]
rs2725185	0.86[EUR][1000 genomes]
rs2725190	0.85[EUR][1000 genomes]
rs2804937	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs34062275	0.87[EUR][1000 genomes]
rs34110351	0.88[EUR][1000 genomes]
rs34289781	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34364659	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34467986	0.88[EUR][1000 genomes]
rs34574986	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34640094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34878380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35341824	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35462783	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35905744	0.88[EUR][1000 genomes]
rs35922675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924984	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs3924985	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4073138	0.86[EUR][1000 genomes]
rs4073139	0.87[EUR][1000 genomes]
rs4128908	0.94[CHB][hapmap]
rs4240498	0.94[CHB][hapmap];0.97[CHD][hapmap]
rs4317904	0.84[CHD][hapmap]
rs4364979	0.86[EUR][1000 genomes]
rs4400713	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4402204	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4403731	0.80[CEU][hapmap];0.94[CHB][hapmap]
rs4421674	0.94[CHB][hapmap];0.94[CHD][hapmap]
rs4445564	1.00[CEU][hapmap];0.92[TSI][hapmap];0.96[EUR][1000 genomes]
rs4468264	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4481947	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4497319	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4508127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4550151	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4600129	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4644582	0.86[EUR][1000 genomes]
rs55947405	0.86[EUR][1000 genomes]
rs56291725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58154726	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58893558	0.86[EUR][1000 genomes]
rs6537493	0.94[CHB][hapmap]
rs6537494	0.94[CHB][hapmap];0.97[CHD][hapmap]
rs67269950	0.88[EUR][1000 genomes]
rs68065270	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7070387	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7073208	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7074818	0.94[CHB][hapmap];0.97[CHD][hapmap]
rs7081243	0.88[EUR][1000 genomes]
rs7084112	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7085823	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7088718	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7097933	0.80[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap]
rs7098134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7100655	0.95[CEU][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs72785015	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7896344	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7897289	0.94[CHB][hapmap]
rs7904272	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7906722	0.94[CHB][hapmap]
rs7907959	0.97[ASN][1000 genomes]
rs7916825	0.94[CHB][hapmap]
rs9804403	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv831866	chr10:50165180-50335276	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	esv2761593	chr10:50276812-50336129	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50266600-50289400	Weak transcription	Colonic Mucosa	Colon
2	chr10:50272600-50294200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr10:50273600-50289800	Weak transcription	NHDF-Ad	bronchial
4	chr10:50279600-50289200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr10:50282400-50289400	Weak transcription	Fetal Kidney	kidney
6	chr10:50283200-50298200	Weak transcription	Spleen	Spleen
7	chr10:50284800-50292400	Enhancers	Liver	Liver
8	chr10:50285200-50292400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr10:50285400-50289200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr10:50285400-50289600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:50286000-50292400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr10:50286800-50289600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr10:50287000-50290200	Enhancers	Fetal Intestine Small	intestine
14	chr10:50287200-50289400	Enhancers	Primary hematopoietic stem cells	blood
15	chr10:50287200-50290000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr10:50287200-50290400	Enhancers	K562	blood
17	chr10:50287200-50292200	Enhancers	Adipose Nuclei	Adipose
18	chr10:50287200-50292400	Enhancers	Brain Substantia Nigra	brain
19	chr10:50287400-50289000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:50287400-50289000	Weak transcription	Lung	lung
21	chr10:50287600-50289000	Enhancers	HSMM	muscle
22	chr10:50287600-50290400	Enhancers	Fetal Intestine Large	intestine
23	chr10:50288000-50291400	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr10:50288000-50291400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr10:50288200-50289200	Enhancers	Stomach Smooth Muscle	stomach
26	chr10:50288200-50289800	Enhancers	Right Atrium	heart
27	chr10:50288200-50291000	Enhancers	Fetal Muscle Leg	muscle
28	chr10:50288200-50291400	Enhancers	Brain Angular Gyrus	brain
29	chr10:50288200-50292000	Enhancers	Fetal Muscle Trunk	muscle
30	chr10:50288200-50292000	Genic enhancers	Fetal Stomach	stomach
31	chr10:50288200-50292200	Enhancers	Colon Smooth Muscle	Colon
32	chr10:50288200-50292200	Enhancers	Left Ventricle	heart
33	chr10:50288200-50292200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr10:50288200-50293200	Enhancers	Right Ventricle	heart
35	chr10:50288400-50289000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr10:50288400-50289000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr10:50288400-50289000	Weak transcription	Fetal Thymus	thymus
38	chr10:50288400-50289600	Enhancers	Aorta	Aorta
39	chr10:50288400-50289600	Enhancers	Pancreas	Pancrea
40	chr10:50288400-50290200	Enhancers	NHLF	lung
41	chr10:50288400-50291000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr10:50288400-50291400	Enhancers	Brain Cingulate Gyrus	brain
43	chr10:50288400-50291600	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr10:50288400-50292400	Enhancers	Brain Hippocampus Middle	brain
45	chr10:50288400-50292600	Enhancers	Brain Anterior Caudate	brain
46	chr10:50288400-50292800	Enhancers	Ovary	ovary
47	chr10:50288400-50293600	Enhancers	HSMMtube	muscle
48	chr10:50288600-50289000	Flanking Active TSS	Fetal Brain Male	brain
49	chr10:50288600-50289000	Enhancers	Rectal Smooth Muscle	rectum
50	chr10:50288600-50289200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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