Variant report

Variant	rs17088840
Chromosome Location	chr9:72753755-72753756
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72748535..72750686-chr9:72751248..72753868,2	MCF-7	breast:

Extended variants
information (count: 160 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs10114215	0.98[ASN][1000 genomes]
rs10511979	0.84[ASN][1000 genomes]
rs1073540	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1112232	0.84[ASN][1000 genomes]
rs11142363	0.91[CHB][hapmap]
rs11142367	0.92[CHB][hapmap]
rs11142368	0.92[CHB][hapmap]
rs11142370	0.92[CHB][hapmap]
rs11142373	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];0.85[JPT][hapmap]
rs1180118	0.92[CHB][hapmap]
rs1180122	0.92[CHB][hapmap]
rs1180124	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1180126	0.92[CHB][hapmap]
rs1180133	0.92[CHB][hapmap]
rs11998951	0.92[CHB][hapmap]
rs12002407	0.84[ASN][1000 genomes]
rs12003971	0.85[ASN][1000 genomes]
rs12006212	0.92[CHB][hapmap]
rs12156606	0.83[CHB][hapmap]
rs12380844	0.92[CHB][hapmap]
rs12683706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12683986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs12684301	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12684987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12685322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12685441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12685491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12685534	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12686312	0.87[AMR][1000 genomes]
rs12686383	0.85[ASN][1000 genomes]
rs12686573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12686584	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12686668	0.84[ASN][1000 genomes]
rs12686850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17051690	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17051696	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17052443	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs17052748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs17087686	0.81[ASN][1000 genomes]
rs17088796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17088889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17088905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1927105	0.86[ASN][1000 genomes]
rs1927110	0.86[ASN][1000 genomes]
rs1927116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1927119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1927142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1927143	0.83[ASN][1000 genomes]
rs1927148	0.92[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1927150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1986412	0.84[ASN][1000 genomes]
rs2001235	0.82[ASN][1000 genomes]
rs2026137	0.92[CHB][hapmap]
rs2026138	0.87[AMR][1000 genomes];0.80[ASN][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];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2148865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2182732	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2296772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2296773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2309584	0.84[ASN][1000 genomes]
rs2871290	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871291	0.81[ASN][1000 genomes]
rs2871295	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2975866	0.85[ASN][1000 genomes]
rs2975867	0.85[ASN][1000 genomes]
rs2975868	0.85[ASN][1000 genomes]
rs2975880	0.86[ASN][1000 genomes]
rs2975884	0.86[ASN][1000 genomes]
rs2997679	0.84[ASN][1000 genomes]
rs2997681	0.81[ASN][1000 genomes]
rs2997714	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3015165	0.82[ASN][1000 genomes]
rs3015169	0.81[ASN][1000 genomes]
rs3015170	0.81[ASN][1000 genomes]
rs3015171	0.83[ASN][1000 genomes]
rs3015173	0.81[ASN][1000 genomes]
rs3015174	0.81[ASN][1000 genomes]
rs3015175	0.82[ASN][1000 genomes]
rs3015177	0.82[ASN][1000 genomes]
rs3015180	0.84[ASN][1000 genomes]
rs3015181	0.84[ASN][1000 genomes]
rs3015182	0.84[ASN][1000 genomes]
rs3015184	0.85[ASN][1000 genomes]
rs3015185	0.85[ASN][1000 genomes]
rs3015186	0.85[ASN][1000 genomes]
rs3015189	0.85[ASN][1000 genomes]
rs3015198	0.86[ASN][1000 genomes]
rs3015204	0.86[ASN][1000 genomes]
rs3015207	0.86[ASN][1000 genomes]
rs3015213	0.86[ASN][1000 genomes]
rs3015223	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34061327	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35188046	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35508139	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3739773	0.87[AMR][1000 genomes]
rs3739774	0.87[AMR][1000 genomes]
rs4069793	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4287005	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4289878	0.85[ASN][1000 genomes]
rs4410968	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4439194	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4449855	0.92[CHB][hapmap]
rs4460447	0.86[ASN][1000 genomes]
rs4495496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4596711	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4602958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4606121	0.87[AMR][1000 genomes]
rs4610818	0.87[AMR][1000 genomes]
rs4621877	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4744982	1.00[ASN][1000 genomes]
rs4744994	0.92[CHB][hapmap]
rs56735283	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56860643	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57048128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57398306	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57477024	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58085049	0.82[ASN][1000 genomes]
rs58219953	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs58948879	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs58969772	0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs58976318	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs59010963	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs59189596	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59444215	0.87[AMR][1000 genomes]
rs59546243	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59589460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59619263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59960592	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs59976188	0.80[ASN][1000 genomes]
rs60049462	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs60391643	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs60458589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61265226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7022893	0.98[ASN][1000 genomes]
rs7034322	0.92[CHB][hapmap]
rs7046167	0.86[AMR][1000 genomes]
rs716535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72710469	0.82[ASN][1000 genomes]
rs72710483	0.85[ASN][1000 genomes]
rs745852	0.86[ASN][1000 genomes]
rs753022	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs753023	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7858988	0.92[CHB][hapmap]
rs7875348	0.80[ASN][1000 genomes]
rs867595	0.82[ASN][1000 genomes]
rs943536	0.92[CHB][hapmap]
rs943540	0.92[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs954808	0.87[AMR][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	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
2	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:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72722000-72758400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:72725800-72764200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:72726800-72785200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:72727000-72776200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:72728200-72758400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:72731200-72768400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:72736200-72761200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr9:72740600-72766400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:72741000-72758600	Weak transcription	Colonic Mucosa	Colon
10	chr9:72741400-72765600	Weak transcription	Esophagus	oesophagus
11	chr9:72741600-72755000	Weak transcription	Left Ventricle	heart
12	chr9:72741600-72757400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr9:72741600-72775400	Weak transcription	Adipose Nuclei	Adipose
14	chr9:72741600-72789400	Weak transcription	Spleen	Spleen
15	chr9:72743000-72754800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:72746200-72755000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr9:72746600-72762600	Weak transcription	Psoas Muscle	Psoas
18	chr9:72748400-72753800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr9:72748600-72762000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr9:72749400-72758400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr9:72749600-72755000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:72749800-72762600	Weak transcription	Fetal Stomach	stomach
23	chr9:72749800-72763000	Weak transcription	Lung	lung
24	chr9:72750200-72753800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr9:72750400-72762600	Weak transcription	Fetal Muscle Leg	muscle
26	chr9:72750400-72771600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:72750600-72754800	Weak transcription	Colon Smooth Muscle	Colon
28	chr9:72750800-72758400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:72751000-72757000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:72751000-72771800	Weak transcription	Aorta	Aorta
31	chr9:72752000-72754800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr9:72752000-72779600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:72752400-72775200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr9:72752600-72771400	Weak transcription	NH-A	brain
35	chr9:72752800-72753800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:72752800-72759400	Weak transcription	HMEC	breast
37	chr9:72753000-72753800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:72753000-72756000	Weak transcription	NHEK	skin
39	chr9:72753200-72753800	Strong transcription	HSMM	muscle
40	chr9:72753200-72754800	Weak transcription	HSMMtube	muscle
41	chr9:72753200-72761000	Weak transcription	Ovary	ovary

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