Variant report

Variant	rs62575842
Chromosome Location	chr9:104298706-104298707
allele	C/G
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	FOS	chr9:104298681-104298976	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr9:104298679-104299008	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr9:104298679-104298980	Hela-S3	cervix:	n/a	n/a
4	FOS	chr9:104298661-104299009	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr9:104298641-104299003	IMR90	lung:	n/a	n/a
6	STAT3	chr9:104298570-104298958	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:104295154..104296821-chr9:104298164..104300262,2	MCF-7	breast:

Variant related genes	Relation type
TMEM246	TF binding region
ENSG00000155827	Chromatin interaction
ENSG00000165152	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10512282	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11788114	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11789610	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11790230	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11790317	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11790832	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11791337	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11793752	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1323432	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16920443	0.93[EUR][1000 genomes]
rs16920462	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17188758	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35681249	0.86[EUR][1000 genomes]
rs57596144	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59782949	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61051202	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61396182	0.93[EUR][1000 genomes]
rs61685305	0.93[EUR][1000 genomes]
rs62575808	0.87[EUR][1000 genomes]
rs62575815	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62575839	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62575844	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62575845	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62575846	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62575847	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62575848	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62575849	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62575850	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62575851	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62575852	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62577397	0.87[EUR][1000 genomes]
rs66786600	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67248872	0.91[AMR][1000 genomes];0.93[EUR][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	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1052492	chr9:104263419-104387782	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv893627	chr9:104268342-104334333	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104296600-104301800	Weak transcription	Spleen	Spleen
2	chr9:104296800-104299000	Weak transcription	Gastric	stomach
3	chr9:104296800-104299200	Weak transcription	Pancreas	Pancrea
4	chr9:104296800-104299400	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr9:104296800-104300400	Enhancers	Fetal Heart	heart
6	chr9:104296800-104300600	Weak transcription	Esophagus	oesophagus
7	chr9:104296800-104302600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:104296800-104302600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:104296800-104302600	Weak transcription	Lung	lung
10	chr9:104296800-104302800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:104296800-104302800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:104296800-104305800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:104296800-104334200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr9:104296800-104337400	Weak transcription	Stomach Mucosa	stomach
15	chr9:104297000-104298800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr9:104297000-104298800	Weak transcription	Right Atrium	heart
17	chr9:104297000-104299000	Weak transcription	Psoas Muscle	Psoas
18	chr9:104297000-104299200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:104297000-104299200	Weak transcription	Ovary	ovary
20	chr9:104297000-104299400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr9:104297000-104302000	Weak transcription	Fetal Stomach	stomach
22	chr9:104297000-104302600	Weak transcription	Colonic Mucosa	Colon
23	chr9:104297000-104302600	Weak transcription	NH-A	brain
24	chr9:104297000-104302800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr9:104297000-104302800	Weak transcription	HSMMtube	muscle
26	chr9:104297000-104309200	Weak transcription	HUVEC	blood vessel
27	chr9:104297000-104317600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr9:104297200-104298800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:104297200-104299000	Weak transcription	Thymus	Thymus
30	chr9:104297200-104299200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr9:104297200-104299200	Weak transcription	Right Ventricle	heart
32	chr9:104297200-104299600	Enhancers	HMEC	breast
33	chr9:104297200-104302400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr9:104297200-104302600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr9:104297200-104302800	Weak transcription	Fetal Intestine Small	intestine
36	chr9:104297200-104309200	Weak transcription	K562	blood
37	chr9:104297400-104298800	Genic enhancers	Primary T cells from cord blood	blood
38	chr9:104297400-104299200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:104297400-104299200	Genic enhancers	A549	lung
40	chr9:104297400-104299400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr9:104297400-104301400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
42	chr9:104297600-104298800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr9:104297600-104298800	Enhancers	Brain Germinal Matrix	brain
44	chr9:104297600-104299200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
45	chr9:104297600-104299400	Genic enhancers	HSMM	muscle
46	chr9:104297600-104299600	Genic enhancers	Brain Angular Gyrus	brain
47	chr9:104297600-104299600	Genic enhancers	Rectal Smooth Muscle	rectum
48	chr9:104297600-104300400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr9:104297600-104300400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr9:104297600-104300800	Genic enhancers	Primary T helper cells fromperipheralblood	blood

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