Variant report

Variant	rs943540
Chromosome Location	chr9:72805675-72805676
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	chr9:72805117..72807381-chr9:72819423..72821508,2	MCF-7	breast:

Extended variants
information (count: 136 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs10114215	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10114223	0.81[AFR][1000 genomes]
rs10125117	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1073540	0.92[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10780869	0.80[AFR][1000 genomes]
rs10868808	0.83[JPT][hapmap]
rs1112937	0.82[YRI][hapmap]
rs11142363	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap]
rs11142367	0.83[JPT][hapmap]
rs11142368	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap]
rs11142370	0.83[JPT][hapmap];0.84[YRI][hapmap]
rs11142373	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap]
rs1180082	0.82[YRI][hapmap]
rs1180084	0.88[YRI][hapmap]
rs1180086	0.80[YRI][hapmap]
rs1180089	0.82[YRI][hapmap]
rs1180091	0.84[YRI][hapmap]
rs1180094	0.80[YRI][hapmap]
rs1180101	0.83[JPT][hapmap];0.84[YRI][hapmap]
rs1180102	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1180104	1.00[CHB][hapmap];0.83[YRI][hapmap]
rs1180105	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1180107	0.83[JPT][hapmap];0.84[YRI][hapmap]
rs1180112	0.83[JPT][hapmap];0.80[YRI][hapmap]
rs1180117	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs1180118	0.83[JPT][hapmap];0.80[YRI][hapmap]
rs1180122	0.83[JPT][hapmap];0.84[YRI][hapmap]
rs1180124	0.87[JPT][hapmap];0.83[YRI][hapmap]
rs1180126	0.83[JPT][hapmap]
rs1180127	0.80[YRI][hapmap]
rs1180133	0.83[JPT][hapmap];0.84[YRI][hapmap]
rs11998951	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12006212	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap]
rs12156606	0.82[JPT][hapmap]
rs12236327	0.80[AFR][1000 genomes]
rs12380844	0.83[JPT][hapmap]
rs12683706	0.82[ASN][1000 genomes]
rs12683986	0.91[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs12684301	0.94[ASN][1000 genomes]
rs12684987	0.82[ASN][1000 genomes]
rs12685322	0.92[ASN][1000 genomes]
rs12685441	0.92[ASN][1000 genomes]
rs12685491	0.92[ASN][1000 genomes]
rs12685534	0.92[ASN][1000 genomes]
rs12686312	0.81[ASN][1000 genomes]
rs12686573	0.82[ASN][1000 genomes]
rs12686584	0.90[ASN][1000 genomes]
rs12686850	0.84[ASN][1000 genomes]
rs17051690	0.94[ASN][1000 genomes]
rs17051696	0.94[ASN][1000 genomes]
rs17052443	0.92[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs17052748	0.92[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs17088796	0.82[ASN][1000 genomes]
rs17088840	0.82[ASN][1000 genomes]
rs17088889	0.82[ASN][1000 genomes]
rs17088905	0.84[ASN][1000 genomes]
rs1887452	0.86[AFR][1000 genomes]
rs1927091	0.81[ASN][1000 genomes]
rs1927093	0.81[ASN][1000 genomes]
rs1927094	0.83[YRI][hapmap]
rs1927116	0.82[ASN][1000 genomes]
rs1927117	0.84[ASN][1000 genomes]
rs1927119	0.84[ASN][1000 genomes]
rs1927125	0.84[AFR][1000 genomes]
rs1927140	0.81[AFR][1000 genomes]
rs1927142	0.91[ASN][1000 genomes]
rs1927143	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1927146	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs1927148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1927150	0.92[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2026137	0.83[JPT][hapmap];0.80[YRI][hapmap]
rs2026138	0.86[ASN][1000 genomes]
rs2148853	0.94[ASN][1000 genomes]
rs2148865	0.84[ASN][1000 genomes]
rs2182732	0.94[ASN][1000 genomes]
rs2182735	0.87[YRI][hapmap]
rs2209781	0.83[AFR][1000 genomes]
rs2309636	0.82[AFR][1000 genomes]
rs2309644	0.80[YRI][hapmap]
rs2871290	0.82[ASN][1000 genomes]
rs2871293	0.83[JPT][hapmap];0.84[YRI][hapmap]
rs2871295	0.94[ASN][1000 genomes]
rs2871296	0.81[ASN][1000 genomes]
rs34061327	0.86[ASN][1000 genomes]
rs35188046	0.82[ASN][1000 genomes]
rs35508139	0.88[ASN][1000 genomes]
rs3739773	0.85[ASN][1000 genomes]
rs3739774	0.83[ASN][1000 genomes]
rs4069793	0.86[ASN][1000 genomes]
rs4287005	0.86[ASN][1000 genomes]
rs4322072	0.86[AFR][1000 genomes]
rs4410968	0.90[ASN][1000 genomes]
rs4439194	0.88[ASN][1000 genomes]
rs4449855	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap]
rs4596711	0.94[ASN][1000 genomes]
rs4602958	0.92[ASN][1000 genomes]
rs4606121	0.85[ASN][1000 genomes]
rs4610818	0.92[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4621877	0.86[ASN][1000 genomes]
rs4744982	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4744986	0.87[AFR][1000 genomes]
rs4744994	0.83[JPT][hapmap]
rs56735283	0.86[ASN][1000 genomes]
rs56860643	0.94[ASN][1000 genomes]
rs57048128	0.86[ASN][1000 genomes]
rs57398306	0.94[ASN][1000 genomes]
rs57477024	0.92[ASN][1000 genomes]
rs58219953	0.86[ASN][1000 genomes]
rs58948879	0.86[ASN][1000 genomes]
rs58969772	0.81[ASN][1000 genomes]
rs58976318	0.86[ASN][1000 genomes]
rs59010963	0.86[ASN][1000 genomes]
rs59189596	0.82[ASN][1000 genomes]
rs59444215	0.84[ASN][1000 genomes]
rs59546243	0.91[ASN][1000 genomes]
rs59589460	0.82[ASN][1000 genomes]
rs59619263	0.82[ASN][1000 genomes]
rs59960592	0.86[ASN][1000 genomes]
rs59976188	0.86[ASN][1000 genomes]
rs60049462	0.86[ASN][1000 genomes]
rs60391643	0.92[ASN][1000 genomes]
rs60458589	0.92[ASN][1000 genomes]
rs61265226	0.84[ASN][1000 genomes]
rs7022893	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7034322	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap]
rs7047789	0.83[YRI][hapmap]
rs716535	0.92[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs753022	0.94[ASN][1000 genomes]
rs753023	0.94[ASN][1000 genomes]
rs7857292	0.84[AFR][1000 genomes]
rs7858988	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap]
rs7875348	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs943536	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap]
rs943539	0.85[AFR][1000 genomes]
rs954808	0.81[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:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72793000-72842600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:72794000-72806800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:72800800-72807800	Weak transcription	Left Ventricle	heart
4	chr9:72800800-72811600	Weak transcription	Esophagus	oesophagus
5	chr9:72801000-72805800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr9:72801000-72810200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:72802000-72806600	Weak transcription	HSMMtube	muscle
8	chr9:72802000-72808200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:72802000-72809000	Weak transcription	Ovary	ovary
10	chr9:72802000-72811000	Weak transcription	Pancreas	Pancrea
11	chr9:72802000-72827000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:72802200-72820000	Weak transcription	Fetal Lung	lung
13	chr9:72803200-72807800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr9:72803400-72810800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:72803600-72808200	Weak transcription	Fetal Brain Male	brain
16	chr9:72803600-72808200	Weak transcription	HSMM	muscle
17	chr9:72804200-72807600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:72804600-72816200	Weak transcription	Adipose Nuclei	Adipose
19	chr9:72804800-72806000	Genic enhancers	Colon Smooth Muscle	Colon
20	chr9:72805200-72820200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:72805600-72805800	Enhancers	Duodenum Smooth Muscle	Duodenum

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