Variant report

Variant	rs10493608
Chromosome Location	chr1:78695253-78695254
allele	A/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	chr1:78694833-78695480	MCF10A-Er-Src	breast:	n/a	n/a
2	CEBPB	chr1:78695053-78695416	IMR90	lung:	n/a	chr1:78695178-78695189 chr1:78695178-78695191
3	MAX	chr1:78695084-78695427	Hela-S3	cervix:	n/a	n/a
4	YY1	chr1:78695009-78695439	SK-N-SH	brain:	n/a	n/a
5	FOSL2	chr1:78695001-78695490	SK-N-SH	brain:	n/a	chr1:78695231-78695242
6	STAT3	chr1:78694916-78695513	MCF10A-Er-Src	breast:	n/a	n/a
7	E2F4	chr1:78694819-78695343	MCF10A-Er-Src	breast:	n/a	n/a
8	JUN	chr1:78695063-78695381	Hela-S3	cervix:	n/a	chr1:78695231-78695242
9	EP300	chr1:78694952-78695432	Hela-S3	cervix:	n/a	chr1:78695176-78695190
10	FOS	chr1:78695039-78695419	MCF10A-Er-Src	breast:	n/a	chr1:78695231-78695242
11	TFAP2A	chr1:78695035-78695502	Hela-S3	cervix:	n/a	chr1:78695202-78695217
12	MAFK	chr1:78695096-78695411	Hela-S3	cervix:	n/a	n/a
13	STAT3	chr1:78694888-78695883	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr1:78695068-78695407	Hela-S3	cervix:	n/a	chr1:78695231-78695242
15	POLR2A	chr1:78694933-78695523	MCF10A-Er-Src	breast:	n/a	n/a
16	SMC3	chr1:78695029-78695424	Hela-S3	cervix:	n/a	n/a
17	FOS	chr1:78694835-78695484	MCF10A-Er-Src	breast:	n/a	chr1:78695231-78695242
18	ZKSCAN1	chr1:78695099-78695478	Hela-S3	cervix:	n/a	n/a
19	NFYA	chr1:78694961-78695389	Hela-S3	cervix:	n/a	n/a
20	FOS	chr1:78694951-78695484	MCF10A-Er-Src	breast:	n/a	chr1:78695231-78695242
21	RFX5	chr1:78695058-78695546	Hela-S3	cervix:	n/a	n/a
22	MYC	chr1:78695048-78695521	MCF10A-Er-Src	breast:	n/a	n/a
23	RAD21	chr1:78695049-78695414	Hela-S3	cervix:	n/a	n/a
24	GTF2F1	chr1:78695041-78695438	Hela-S3	cervix:	n/a	n/a
25	CEBPB	chr1:78694932-78695481	Hela-S3	cervix:	n/a	chr1:78695178-78695189 chr1:78695178-78695191
26	TBP	chr1:78695023-78695413	Hela-S3	cervix:	n/a	n/a
27	MYC	chr1:78694995-78695468	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr1:78695139-78695442	MCF10A-Er-Src	breast:	n/a	n/a
29	STAT3	chr1:78695024-78695413	Hela-S3	cervix:	n/a	n/a
30	JUND	chr1:78695046-78695471	Hela-S3	cervix:	n/a	chr1:78695231-78695242
31	FOS	chr1:78694845-78695427	MCF10A-Er-Src	breast:	n/a	chr1:78695231-78695242
32	BRCA1	chr1:78695045-78695501	Hela-S3	cervix:	n/a	n/a
33	RCOR1	chr1:78695077-78695462	Hela-S3	cervix:	n/a	n/a
34	STAT3	chr1:78694922-78695510	MCF10A-Er-Src	breast:	n/a	n/a
35	TFAP2C	chr1:78695028-78695394	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ENSG00000237413	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10873967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11162435	0.85[EUR][1000 genomes]
rs11162436	0.85[EUR][1000 genomes]
rs1323096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1323097	0.85[EUR][1000 genomes]
rs1323098	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1323099	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1770303	0.87[ASN][1000 genomes]
rs1770311	0.92[ASN][1000 genomes]
rs1770313	0.92[ASN][1000 genomes]
rs2181453	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2351912	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4650620	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs593113	0.82[ASN][1000 genomes]
rs600237	0.92[ASN][1000 genomes]
rs658377	0.92[ASN][1000 genomes]
rs669357	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs669764	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs671229	0.92[ASN][1000 genomes]
rs672620	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78689800-78697800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:78689800-78702400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:78689800-78703000	Weak transcription	Pancreas	Pancrea
4	chr1:78694000-78695800	Enhancers	Hela-S3	cervix
5	chr1:78694400-78695800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:78694600-78695400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:78694600-78695600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
8	chr1:78694600-78695600	Enhancers	HMEC	breast
9	chr1:78694600-78695800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:78694600-78699800	Weak transcription	Brain Germinal Matrix	brain
11	chr1:78694800-78695400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:78694800-78695400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:78694800-78695600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:78694800-78695800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:78694800-78695800	Enhancers	Osteobl	bone
16	chr1:78695000-78695600	Enhancers	NHDF-Ad	bronchial
17	chr1:78695200-78695400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
18	chr1:78695200-78695400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
19	chr1:78695200-78695400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
20	chr1:78695200-78697600	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links