Variant report

Variant	rs4979166
Chromosome Location	chr9:115610148-115610149
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	chr9:115609355..115610986-chr9:115659802..115661844,2	MCF-7	breast:
2	chr9:115605264..115607754-chr9:115609316..115612065,2	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10117017	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs10117709	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs10122712	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs10481638	1.00[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10481671	0.87[CEU][hapmap]
rs10732374	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.90[ASN][1000 genomes]
rs10733595	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs10733596	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10733597	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10739371	0.93[CEU][hapmap];0.87[TSI][hapmap];0.85[ASN][1000 genomes]
rs10739375	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10759587	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs10759588	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs10759589	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10759591	0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10759592	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10759593	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10759596	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10759597	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10759598	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10759599	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10759600	1.00[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10759601	1.00[CEU][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10817391	0.89[ASN][1000 genomes]
rs10817392	0.87[ASN][1000 genomes]
rs10817395	0.89[ASN][1000 genomes]
rs10817396	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10817397	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10817398	1.00[CEU][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10817399	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10817400	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10817401	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10817402	0.87[CEU][hapmap]
rs10981513	0.89[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs10981515	0.83[ASN][1000 genomes]
rs10981516	0.89[ASN][1000 genomes]
rs10981519	0.89[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs10981521	0.89[ASN][1000 genomes]
rs10981522	0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs10981523	0.89[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs11791125	0.89[ASN][1000 genomes]
rs11793016	0.89[ASN][1000 genomes]
rs1418408	0.93[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs1475292	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1539340	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1539341	0.84[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1539342	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1539345	0.90[ASN][1000 genomes]
rs1970527	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1970528	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2000204	0.83[ASN][1000 genomes]
rs2153839	0.85[ASN][1000 genomes]
rs2185767	0.89[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2645988	0.93[CEU][hapmap]
rs2796024	0.93[CEU][hapmap];0.83[ASN][1000 genomes]
rs4276760	0.89[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs4366151	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4367629	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4978504	0.84[ASN][1000 genomes]
rs4979158	0.93[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs4979162	0.90[ASN][1000 genomes]
rs4979163	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.93[ASN][1000 genomes]
rs4979164	0.93[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs4979167	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4979168	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57546880	0.89[ASN][1000 genomes]
rs57672123	0.89[ASN][1000 genomes]
rs59645636	0.89[ASN][1000 genomes]
rs60989307	0.89[ASN][1000 genomes]
rs61626147	0.84[ASN][1000 genomes]
rs6477960	0.83[ASN][1000 genomes]
rs6477961	0.90[ASN][1000 genomes]
rs7030460	0.85[ASN][1000 genomes]
rs7032401	0.84[ASN][1000 genomes]
rs7032763	0.87[CEU][hapmap]
rs7856199	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs7871799	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs787282	0.83[ASN][1000 genomes]
rs787283	0.93[CEU][hapmap];0.83[ASN][1000 genomes]
rs787288	0.93[CEU][hapmap];0.83[ASN][1000 genomes]
rs7873644	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs870078	0.83[ASN][1000 genomes]
rs883462	0.89[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs912661	0.86[CEU][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9299210	0.88[ASN][1000 genomes]
rs9299211	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9299212	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs999018	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv893733	chr9:115397206-115712068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv2422302	chr9:115550339-115656433	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv2757351	chr9:115600623-115632898	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115577600-115630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr9:115582400-115630000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr9:115591400-115623200	Weak transcription	Fetal Heart	heart
4	chr9:115593200-115611000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr9:115594200-115610800	Weak transcription	Esophagus	oesophagus
6	chr9:115594200-115616000	Weak transcription	Small Intestine	intestine
7	chr9:115594200-115620400	Weak transcription	Thymus	Thymus
8	chr9:115594200-115634400	Weak transcription	NH-A	brain
9	chr9:115594400-115626800	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:115596400-115613600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr9:115598600-115615200	Weak transcription	Psoas Muscle	Psoas
12	chr9:115598800-115610600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:115598800-115613200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr9:115599000-115623200	Weak transcription	Right Ventricle	heart
15	chr9:115599400-115610600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:115599400-115612000	Weak transcription	Pancreas	Pancrea
17	chr9:115599400-115612800	Weak transcription	Placenta	Placenta
18	chr9:115599400-115613000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr9:115599400-115615200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:115599400-115623600	Weak transcription	Right Atrium	heart
21	chr9:115599400-115625200	Weak transcription	Colonic Mucosa	Colon
22	chr9:115601000-115610600	Weak transcription	Spleen	Spleen
23	chr9:115601000-115612400	Weak transcription	Aorta	Aorta
24	chr9:115601200-115641200	Weak transcription	Fetal Brain Male	brain
25	chr9:115601400-115612800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr9:115601600-115610600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:115601600-115620600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:115601800-115613000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr9:115602000-115620600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:115602200-115613200	Weak transcription	Left Ventricle	heart
31	chr9:115602400-115610800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr9:115602400-115611600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:115602400-115612400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:115602400-115613000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr9:115602400-115613200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr9:115602400-115613400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:115602600-115610600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr9:115602600-115611000	Weak transcription	Fetal Lung	lung
39	chr9:115602600-115612800	Weak transcription	Ovary	ovary
40	chr9:115602600-115614600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr9:115602600-115615200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr9:115602600-115626600	Weak transcription	Brain Germinal Matrix	brain
43	chr9:115602600-115626800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:115603000-115612200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr9:115604000-115610800	Weak transcription	Fetal Stomach	stomach
46	chr9:115604000-115613200	Weak transcription	Fetal Brain Female	brain
47	chr9:115604000-115613200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr9:115604000-115626600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr9:115604200-115621200	Weak transcription	HepG2	liver
50	chr9:115604400-115610600	Weak transcription	Stomach Smooth Muscle	stomach

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