Variant report

Variant	rs2871295
Chromosome Location	chr9:72810984-72810985
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	chr9:72748007..72750453-chr9:72808216..72811141,2	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10114215	0.86[ASN][1000 genomes]
rs10491653	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1073540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11142363	0.91[CHB][hapmap]
rs11142368	0.92[CHB][hapmap]
rs11142373	0.92[CHB][hapmap]
rs1180102	0.92[CHB][hapmap]
rs1180104	0.92[CHB][hapmap]
rs1180105	0.92[CHB][hapmap]
rs1180117	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs1180124	0.81[JPT][hapmap]
rs11998951	0.92[CHB][hapmap]
rs12006212	0.92[CHB][hapmap]
rs12683706	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12683986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12684301	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12684987	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12685322	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12685441	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12685491	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12685534	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12686312	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12686573	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12686584	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12686850	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17051690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17052748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17053503	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17053650	0.86[AFR][1000 genomes]
rs17088796	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17088840	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17088889	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17088905	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1927116	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1927117	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1927119	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1927142	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1927143	0.91[ASN][1000 genomes]
rs1927148	0.92[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1927150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2026138	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2094400	0.87[AMR][1000 genomes]
rs2148853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148865	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2182731	0.81[ASN][1000 genomes]
rs2182732	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296772	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2296773	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2871290	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3015223	1.00[AMR][1000 genomes]
rs34061327	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35188046	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35508139	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3739773	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3739774	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4069793	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4287005	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4410968	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4439194	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4449855	0.92[CHB][hapmap]
rs4495496	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4596711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4602958	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4606121	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4610818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4621877	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4744982	0.88[ASN][1000 genomes]
rs56735283	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56860643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57048128	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57398306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57477024	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58219953	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58662316	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58948879	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58969772	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58976318	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59010963	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59189596	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59444215	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59546243	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59589460	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59619263	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59960592	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59976188	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60049462	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60391643	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60458589	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61092050	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs61265226	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7022893	0.86[ASN][1000 genomes]
rs7034322	0.92[CHB][hapmap]
rs7046167	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs716535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs753022	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753023	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858988	0.92[CHB][hapmap]
rs7875348	0.88[ASN][1000 genomes]
rs943536	0.92[CHB][hapmap]
rs943540	0.92[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs954808	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72793000-72842600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:72800800-72811600	Weak transcription	Esophagus	oesophagus
3	chr9:72802000-72811000	Weak transcription	Pancreas	Pancrea
4	chr9:72802000-72827000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:72802200-72820000	Weak transcription	Fetal Lung	lung
6	chr9:72804600-72816200	Weak transcription	Adipose Nuclei	Adipose
7	chr9:72805200-72820200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:72806400-72819600	Weak transcription	Liver	Liver
9	chr9:72807600-72813800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:72807800-72812000	Strong transcription	Stomach Smooth Muscle	stomach
11	chr9:72808000-72819600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:72808000-72819600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:72808000-72820000	Weak transcription	HMEC	breast
14	chr9:72808000-72820400	Weak transcription	Left Ventricle	heart
15	chr9:72808200-72812200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr9:72808200-72813000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:72808200-72820000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr9:72809000-72811400	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:72809000-72813000	Strong transcription	HSMMtube	muscle
20	chr9:72809400-72820400	Weak transcription	HSMM	muscle
21	chr9:72809600-72837800	Weak transcription	NH-A	brain
22	chr9:72810200-72811800	Strong transcription	Ovary	ovary
23	chr9:72810800-72812400	Weak transcription	NHDF-Ad	bronchial
24	chr9:72810800-72827800	Weak transcription	Colon Smooth Muscle	Colon

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