Variant report

Variant	rs17088796
Chromosome Location	chr9:72748304-72748305
allele	A/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: 145 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs10114215	0.98[ASN][1000 genomes]
rs10511979	0.84[ASN][1000 genomes]
rs1073540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1112232	0.84[ASN][1000 genomes]
rs11142363	0.91[CHB][hapmap]
rs11142368	0.92[CHB][hapmap]
rs1180102	0.92[CHB][hapmap]
rs1180104	0.92[CHB][hapmap]
rs1180105	0.92[CHB][hapmap]
rs1180117	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs1180124	0.83[JPT][hapmap]
rs11998951	0.92[CHB][hapmap]
rs12002407	0.84[ASN][1000 genomes]
rs12003971	0.85[ASN][1000 genomes]
rs12006212	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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs17088840	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]
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]
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]

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:55 , 50 per page) page: 1 2

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	chr9:72726200-72749200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:72726800-72785200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:72727000-72776200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr9:72728200-72752800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr9:72728200-72758400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr9:72731200-72768400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:72733800-72748400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:72736200-72748800	Weak transcription	Fetal Brain Female	brain
11	chr9:72736200-72761200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:72738200-72750400	Weak transcription	Fetal Intestine Small	intestine
13	chr9:72739000-72749000	Weak transcription	Gastric	stomach
14	chr9:72740400-72750000	Weak transcription	NH-A	brain
15	chr9:72740600-72766400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:72741000-72758600	Weak transcription	Colonic Mucosa	Colon
17	chr9:72741400-72765600	Weak transcription	Esophagus	oesophagus
18	chr9:72741600-72749400	Weak transcription	Fetal Stomach	stomach
19	chr9:72741600-72751600	Weak transcription	NHLF	lung
20	chr9:72741600-72755000	Weak transcription	Left Ventricle	heart
21	chr9:72741600-72757400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:72741600-72775400	Weak transcription	Adipose Nuclei	Adipose
23	chr9:72741600-72789400	Weak transcription	Spleen	Spleen
24	chr9:72742800-72748800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:72743000-72754800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:72743400-72748400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:72745600-72749600	Weak transcription	Lung	lung
28	chr9:72746200-72749200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:72746200-72755000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr9:72746600-72750600	Weak transcription	HMEC	breast
31	chr9:72746600-72762600	Weak transcription	Psoas Muscle	Psoas
32	chr9:72746800-72748400	Weak transcription	Fetal Heart	heart
33	chr9:72746800-72750200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:72746800-72750200	Weak transcription	NHEK	skin
35	chr9:72746800-72750400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:72747400-72752600	Enhancers	HSMM	muscle
37	chr9:72747800-72753400	Enhancers	NHDF-Ad	bronchial
38	chr9:72748000-72748400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr9:72748000-72748600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:72748000-72749600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:72748000-72749800	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr9:72748000-72750200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr9:72748000-72750400	Enhancers	Fetal Muscle Leg	muscle
44	chr9:72748000-72751400	Enhancers	Osteobl	bone
45	chr9:72748000-72752800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr9:72748200-72748600	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr9:72748200-72748800	Enhancers	Aorta	Aorta
48	chr9:72748200-72749200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr9:72748200-72749200	Genic enhancers	Colon Smooth Muscle	Colon
50	chr9:72748200-72749200	Genic enhancers	Ovary	ovary

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