Variant report

Variant	rs62576412
Chromosome Location	chr9:115580729-115580730
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	chr9:115568430..115571071-chr9:115577497..115580948,3	MCF-7	breast:
2	chr9:115471879..115473939-chr9:115578770..115581300,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10513169	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817391	0.88[EUR][1000 genomes]
rs10817392	0.88[EUR][1000 genomes]
rs10817395	0.88[EUR][1000 genomes]
rs10981493	0.86[ASN][1000 genomes]
rs10981513	0.96[EUR][1000 genomes]
rs10981516	0.88[EUR][1000 genomes]
rs10981519	0.88[EUR][1000 genomes]
rs10981521	0.88[EUR][1000 genomes]
rs10981522	0.88[EUR][1000 genomes]
rs10981523	0.88[EUR][1000 genomes]
rs10981530	0.82[EUR][1000 genomes]
rs10981531	0.82[EUR][1000 genomes]
rs11791125	0.88[EUR][1000 genomes]
rs11793016	0.88[EUR][1000 genomes]
rs1573055	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573056	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17742501	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17742994	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17743418	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17743824	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17821593	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185767	0.86[EUR][1000 genomes]
rs2645988	0.93[ASN][1000 genomes]
rs41280189	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4276760	0.86[EUR][1000 genomes]
rs4574920	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57546880	0.88[EUR][1000 genomes]
rs57672123	0.88[EUR][1000 genomes]
rs58247585	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59645636	0.88[EUR][1000 genomes]
rs60989307	0.88[EUR][1000 genomes]
rs61626147	0.88[EUR][1000 genomes]
rs62576361	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576362	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62576365	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576366	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576369	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576370	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576371	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576383	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576384	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576385	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576386	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576389	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576390	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576391	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576392	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576393	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576394	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576395	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576396	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576405	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576406	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576407	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576409	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576410	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576411	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576413	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576414	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576415	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576438	0.82[EUR][1000 genomes]
rs7467129	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs883462	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 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	nsv515899	chr9:115359049-115593870	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv34346	chr9:115360505-115581453	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1038999	chr9:115367078-115590950	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv2757350	chr9:115371397-115594108	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	esv2761275	chr9:115376461-115590962	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1049451	chr9:115378282-115585109	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1047374	chr9:115378282-115590950	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1038306	chr9:115379305-115595695	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv540194	chr9:115379305-115595695	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1051909	chr9:115379505-115588377	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv540195	chr9:115379505-115588377	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv915763	chr9:115379600-115588349	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv515121	chr9:115383227-115585827	Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv1044168	chr9:115383253-115585109	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv1048327	chr9:115383253-115589646	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats 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	15 gene(s)	inside rSNPs	diseases
18	nsv1044381	chr9:115383253-115590950	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
19	nsv442163	chr9:115383255-115590578	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
20	esv34763	chr9:115383332-115581453	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
21	nsv430090	chr9:115383445-115594445	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	nsv1041424	chr9:115389428-115590950	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
23	nsv1047625	chr9:115390759-115587347	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats 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	15 gene(s)	inside rSNPs	diseases
24	nsv540196	chr9:115390759-115587347	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
25	nsv615198	chr9:115397206-115589251	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
26	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
27	nsv1051808	chr9:115397891-115590950	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
28	esv34739	chr9:115409445-115581453	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
29	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

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115549800-115593600	Weak transcription	Thymus	Thymus
2	chr9:115552800-115593800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:115553000-115582000	Weak transcription	Esophagus	oesophagus
4	chr9:115555800-115581800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr9:115555800-115582000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:115555800-115582000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:115555800-115597400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr9:115558800-115581800	Weak transcription	Aorta	Aorta
9	chr9:115559400-115581800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr9:115559400-115598400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:115559600-115593800	Weak transcription	Brain Germinal Matrix	brain
12	chr9:115564600-115593600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr9:115565000-115600800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr9:115565600-115600800	Weak transcription	HMEC	breast
15	chr9:115566800-115598000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr9:115567000-115580800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr9:115567400-115581200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr9:115567400-115586200	Weak transcription	Colonic Mucosa	Colon
19	chr9:115569600-115593800	Weak transcription	Fetal Brain Female	brain
20	chr9:115570400-115581000	Weak transcription	Primary T cells from cord blood	blood
21	chr9:115570400-115583400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr9:115570600-115584800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr9:115570600-115608400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr9:115570800-115593600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr9:115573000-115582000	Weak transcription	Fetal Lung	lung
26	chr9:115573000-115593800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr9:115573200-115582000	Weak transcription	Right Ventricle	heart
28	chr9:115573200-115593200	Weak transcription	Left Ventricle	heart
29	chr9:115573200-115593200	Weak transcription	Spleen	Spleen
30	chr9:115573200-115593800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:115573200-115598400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr9:115573400-115582000	Weak transcription	Lung	lung
33	chr9:115573400-115583200	Weak transcription	NHEK	skin
34	chr9:115573400-115595600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr9:115573400-115598800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr9:115573600-115581800	Weak transcription	HSMMtube	muscle
37	chr9:115573600-115598400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:115573600-115607800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr9:115573800-115582200	Weak transcription	Placenta	Placenta
40	chr9:115574000-115593800	Weak transcription	HepG2	liver
41	chr9:115574000-115598600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr9:115574200-115582000	Weak transcription	Brain Anterior Caudate	brain
43	chr9:115574400-115582000	Weak transcription	Brain Angular Gyrus	brain
44	chr9:115574400-115582000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr9:115574400-115582000	Weak transcription	K562	blood
46	chr9:115574400-115585000	Weak transcription	Stomach Mucosa	stomach
47	chr9:115575000-115600800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr9:115577600-115630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr9:115577800-115594000	Weak transcription	NH-A	brain
50	chr9:115578400-115580800	Enhancers	Brain Cingulate Gyrus	brain

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