Variant report

Variant	rs62576438
Chromosome Location	chr9:115614957-115614958
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr9:115614888-115615351	MCF10A-Er-Src	breast:	n/a	chr9:115615092-115615103 chr9:115615088-115615108
2	STAT3	chr9:115614881-115615456	MCF10A-Er-Src	breast:	n/a	chr9:115615092-115615103 chr9:115615088-115615108
3	STAT3	chr9:115614878-115615384	MCF10A-Er-Src	breast:	n/a	chr9:115615092-115615103 chr9:115615088-115615108

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:115612240..115614238-chr9:115614501..115616948,2	K562	blood:
2	chr9:115614764..115617679-chr9:115622672..115625535,2	K562	blood:

Variant related genes	Relation type
SNX30	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10513169	0.87[EUR][1000 genomes]
rs10817391	0.86[EUR][1000 genomes]
rs10817392	0.86[EUR][1000 genomes]
rs10817395	0.86[EUR][1000 genomes]
rs10981516	0.86[EUR][1000 genomes]
rs10981519	0.86[EUR][1000 genomes]
rs10981521	0.86[EUR][1000 genomes]
rs10981522	0.86[EUR][1000 genomes]
rs10981523	0.86[EUR][1000 genomes]
rs10981530	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981531	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981532	0.87[EUR][1000 genomes]
rs10981533	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11791125	0.86[EUR][1000 genomes]
rs11793016	0.86[EUR][1000 genomes]
rs1573055	0.86[EUR][1000 genomes]
rs1573056	0.87[EUR][1000 genomes]
rs16917440	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17743418	0.87[EUR][1000 genomes]
rs17743824	0.89[EUR][1000 genomes]
rs2185767	0.84[EUR][1000 genomes]
rs41280189	0.89[EUR][1000 genomes]
rs41280193	0.80[EUR][1000 genomes]
rs4276760	0.84[EUR][1000 genomes]
rs57546880	0.86[EUR][1000 genomes]
rs57672123	0.86[EUR][1000 genomes]
rs58247585	0.89[EUR][1000 genomes]
rs59645636	0.86[EUR][1000 genomes]
rs60989307	0.86[EUR][1000 genomes]
rs61626147	0.86[EUR][1000 genomes]
rs62576412	0.82[EUR][1000 genomes]
rs62576413	0.87[EUR][1000 genomes]
rs62576414	0.87[EUR][1000 genomes]
rs62576415	0.87[EUR][1000 genomes]
rs62576456	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62577669	0.80[EUR][1000 genomes]
rs62577670	0.80[EUR][1000 genomes]
rs883462	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv1047000	chr9:115610445-115884038	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 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	chr9:115594200-115616000	Weak transcription	Small Intestine	intestine
5	chr9:115594200-115620400	Weak transcription	Thymus	Thymus
6	chr9:115594200-115634400	Weak transcription	NH-A	brain
7	chr9:115594400-115626800	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:115598600-115615200	Weak transcription	Psoas Muscle	Psoas
9	chr9:115599000-115623200	Weak transcription	Right Ventricle	heart
10	chr9:115599400-115615200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:115599400-115623600	Weak transcription	Right Atrium	heart
12	chr9:115599400-115625200	Weak transcription	Colonic Mucosa	Colon
13	chr9:115601200-115641200	Weak transcription	Fetal Brain Male	brain
14	chr9:115601600-115620600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:115602000-115620600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr9:115602600-115615200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr9:115602600-115626600	Weak transcription	Brain Germinal Matrix	brain
18	chr9:115602600-115626800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:115604000-115626600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr9:115604200-115621200	Weak transcription	HepG2	liver
21	chr9:115607400-115643400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:115607600-115615000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr9:115607600-115615000	Weak transcription	HMEC	breast
24	chr9:115607600-115620800	Strong transcription	Fetal Intestine Small	intestine
25	chr9:115607600-115630200	Weak transcription	NHEK	skin
26	chr9:115608600-115617000	Strong transcription	Fetal Intestine Large	intestine
27	chr9:115609200-115615200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:115609400-115615000	Weak transcription	Brain Angular Gyrus	brain
29	chr9:115609400-115615400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:115609400-115623200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr9:115609800-115615400	Weak transcription	HSMM	muscle
32	chr9:115610400-115615400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr9:115610400-115615600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:115610800-115615200	Strong transcription	Fetal Stomach	stomach
35	chr9:115611400-115615000	Weak transcription	Esophagus	oesophagus
36	chr9:115611400-115615400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr9:115611400-115628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr9:115611400-115634600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr9:115611600-115616800	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr9:115611600-115619000	Weak transcription	Fetal Lung	lung
41	chr9:115611600-115626800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr9:115611600-115630200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr9:115611600-115634200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr9:115611800-115616000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr9:115611800-115617000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr9:115611800-115617000	Strong transcription	Stomach Smooth Muscle	stomach
47	chr9:115611800-115630200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr9:115612000-115615000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr9:115612000-115617000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr9:115612000-115620600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links