Variant report

Variant	rs2296773
Chromosome Location	chr9:72741298-72741299
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	chr9:72733654..72736603-chr9:72737665..72741649,3	MCF-7	breast:

Extended variants
information (count: 161 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:160)

rs_ID	r²[population]
rs10114215	0.89[ASN][1000 genomes]
rs10511979	0.92[ASN][1000 genomes]
rs1073540	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes]
rs1112232	0.92[ASN][1000 genomes]
rs11142363	0.91[CHB][hapmap]
rs11142367	0.92[CHB][hapmap]
rs11142368	0.92[CHB][hapmap]
rs1180101	0.92[CHB][hapmap]
rs1180102	0.92[CHB][hapmap]
rs1180104	0.92[CHB][hapmap]
rs1180105	0.92[CHB][hapmap]
rs1180107	0.92[CHB][hapmap]
rs1180112	0.91[CHB][hapmap]
rs1180117	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs1180118	0.92[CHB][hapmap]
rs1180122	0.92[CHB][hapmap]
rs1180124	0.91[CHB][hapmap]
rs1180126	0.92[CHB][hapmap]
rs1180133	0.92[CHB][hapmap]
rs11998951	0.92[CHB][hapmap]
rs12002407	0.92[ASN][1000 genomes]
rs12003971	0.93[ASN][1000 genomes]
rs12006212	0.92[CHB][hapmap]
rs12380844	0.92[CHB][hapmap]
rs12683706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12683986	1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes]
rs12684301	1.00[AMR][1000 genomes]
rs12684987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12685322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12685441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12685491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12685534	1.00[AMR][1000 genomes]
rs12685632	0.84[ASN][1000 genomes]
rs12685937	0.82[ASN][1000 genomes]
rs12685939	0.84[ASN][1000 genomes]
rs12686312	0.87[AMR][1000 genomes]
rs12686383	0.93[ASN][1000 genomes]
rs12686573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12686584	0.87[AMR][1000 genomes]
rs12686668	0.92[ASN][1000 genomes]
rs12686850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17051690	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051696	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17052443	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes]
rs17052748	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes]
rs17087686	0.87[ASN][1000 genomes]
rs17088796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17088840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17088889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17088905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17523363	0.84[ASN][1000 genomes]
rs1927105	0.95[ASN][1000 genomes]
rs1927110	0.95[ASN][1000 genomes]
rs1927116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1927117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1927119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1927142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1927148	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs1927150	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1986412	0.92[ASN][1000 genomes]
rs2001235	0.90[ASN][1000 genomes]
rs2026137	0.92[CHB][hapmap]
rs2026138	0.87[AMR][1000 genomes]
rs2094399	0.83[AFR][1000 genomes]
rs2094400	0.87[AMR][1000 genomes]
rs2148853	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2148865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2182732	1.00[AMR][1000 genomes]
rs2296772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309584	0.92[ASN][1000 genomes]
rs2871290	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2871295	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2975866	0.93[ASN][1000 genomes]
rs2975867	0.93[ASN][1000 genomes]
rs2975868	0.93[ASN][1000 genomes]
rs2975880	0.95[ASN][1000 genomes]
rs2975884	0.95[ASN][1000 genomes]
rs2975911	0.84[ASN][1000 genomes]
rs2997668	0.86[ASN][1000 genomes]
rs2997679	0.92[ASN][1000 genomes]
rs2997681	0.89[ASN][1000 genomes]
rs2997714	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3015165	0.88[ASN][1000 genomes]
rs3015169	0.89[ASN][1000 genomes]
rs3015170	0.89[ASN][1000 genomes]
rs3015171	0.87[ASN][1000 genomes]
rs3015173	0.89[ASN][1000 genomes]
rs3015174	0.89[ASN][1000 genomes]
rs3015175	0.90[ASN][1000 genomes]
rs3015177	0.90[ASN][1000 genomes]
rs3015180	0.92[ASN][1000 genomes]
rs3015181	0.92[ASN][1000 genomes]
rs3015182	0.92[ASN][1000 genomes]
rs3015184	0.93[ASN][1000 genomes]
rs3015185	0.93[ASN][1000 genomes]
rs3015186	0.93[ASN][1000 genomes]
rs3015189	0.93[ASN][1000 genomes]
rs3015198	0.95[ASN][1000 genomes]
rs3015204	0.95[ASN][1000 genomes]
rs3015207	0.95[ASN][1000 genomes]
rs3015213	0.95[ASN][1000 genomes]
rs3015223	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34061327	0.87[AMR][1000 genomes]
rs35188046	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35508139	0.87[AMR][1000 genomes]
rs3739773	0.87[AMR][1000 genomes]
rs3739774	0.87[AMR][1000 genomes]
rs3829096	0.83[ASN][1000 genomes]
rs4069793	0.87[AMR][1000 genomes]
rs4287005	0.87[AMR][1000 genomes]
rs4289878	0.93[ASN][1000 genomes]
rs4410968	1.00[AMR][1000 genomes]
rs4439194	1.00[AMR][1000 genomes]
rs4449855	0.92[CHB][hapmap]
rs4460447	0.95[ASN][1000 genomes]
rs4495496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4596711	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4602958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4606121	0.87[AMR][1000 genomes]
rs4621877	0.87[AMR][1000 genomes]
rs4744982	0.91[ASN][1000 genomes]
rs4744994	0.92[CHB][hapmap]
rs56735283	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56860643	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57048128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57398306	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57477024	0.93[AMR][1000 genomes]
rs58085049	0.90[ASN][1000 genomes]
rs58219953	0.87[AMR][1000 genomes]
rs58660710	0.84[ASN][1000 genomes]
rs58948879	0.87[AMR][1000 genomes]
rs58969772	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58976318	0.87[AMR][1000 genomes]
rs59010963	0.87[AMR][1000 genomes]
rs59189596	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59444215	0.87[AMR][1000 genomes]
rs59546243	0.87[AMR][1000 genomes]
rs59589460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59619263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59960592	0.81[AMR][1000 genomes]
rs60049462	0.87[AMR][1000 genomes]
rs60391643	0.93[AMR][1000 genomes]
rs60458589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61265226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61416419	0.86[ASN][1000 genomes]
rs7022893	0.89[ASN][1000 genomes]
rs7034322	0.92[CHB][hapmap]
rs7046167	0.86[AMR][1000 genomes]
rs716535	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes]
rs72709197	0.84[ASN][1000 genomes]
rs72709200	0.84[ASN][1000 genomes]
rs72710469	0.90[ASN][1000 genomes]
rs72710483	0.93[ASN][1000 genomes]
rs745852	0.95[ASN][1000 genomes]
rs753022	1.00[AMR][1000 genomes]
rs753023	1.00[AMR][1000 genomes]
rs7858988	0.92[CHB][hapmap]
rs867595	0.90[ASN][1000 genomes]
rs943536	0.92[CHB][hapmap]
rs943540	0.92[CHB][hapmap];0.91[JPT][hapmap]

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	nsv1049457	chr9:72539144-72765913	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers 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:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72714800-72742400	Weak transcription	Aorta	Aorta
2	chr9:72722000-72758400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:72724400-72742600	Weak transcription	Right Ventricle	heart
4	chr9:72725600-72745200	Weak transcription	Lung	lung
5	chr9:72725800-72742600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:72725800-72764200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:72726200-72749200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr9:72726800-72785200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr9:72727000-72776200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr9:72727200-72746600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:72728200-72752800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr9:72728200-72758400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr9:72728600-72746800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr9:72729200-72744800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr9:72731200-72768400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:72733200-72745000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr9:72733800-72748400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:72736200-72745000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr9:72736200-72746000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr9:72736200-72747400	Weak transcription	Fetal Muscle Leg	muscle
21	chr9:72736200-72748800	Weak transcription	Fetal Brain Female	brain
22	chr9:72736200-72761200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr9:72736600-72744600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr9:72737000-72744200	Strong transcription	Colon Smooth Muscle	Colon
25	chr9:72737000-72748000	Strong transcription	Stomach Smooth Muscle	stomach
26	chr9:72737200-72745200	Strong transcription	HSMMtube	muscle
27	chr9:72737600-72741400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:72737600-72741400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:72737800-72742000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr9:72738000-72742600	Enhancers	HepG2	liver
31	chr9:72738200-72750400	Weak transcription	Fetal Intestine Small	intestine
32	chr9:72738400-72741800	Enhancers	Pancreas	Pancrea
33	chr9:72739000-72749000	Weak transcription	Gastric	stomach
34	chr9:72739600-72741600	Strong transcription	Adipose Nuclei	Adipose
35	chr9:72739800-72741600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr9:72739800-72741600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:72739800-72741800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr9:72740000-72741400	Enhancers	NHEK	skin
39	chr9:72740000-72743400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:72740200-72741600	Enhancers	Ovary	ovary
41	chr9:72740200-72746200	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr9:72740400-72741400	Enhancers	Esophagus	oesophagus
43	chr9:72740400-72741600	Enhancers	Placenta Amnion	Placenta Amnion
44	chr9:72740400-72741600	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr9:72740400-72743200	Enhancers	Fetal Lung	lung
46	chr9:72740400-72750000	Weak transcription	NH-A	brain
47	chr9:72740600-72741800	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr9:72740600-72766400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr9:72740800-72741600	Genic enhancers	NHLF	lung
50	chr9:72740800-72744000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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