Variant report

Variant	rs2762109
Chromosome Location	chr13:94051889-94051890
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	POLR2A	chr13:94051769-94052191	PFSK-1	brain:	n/a	n/a
2	FOSL2	chr13:94051581-94052064	A549	lung:	n/a	chr13:94051856-94051865 chr13:94051858-94051869 chr13:94051855-94051866
3	MYC	chr13:94051789-94052082	MCF10A-Er-Src	breast:	n/a	chr13:94051944-94051957 chr13:94051945-94051954 chr13:94051857-94051866 chr13:94051946-94051956 chr13:94051945-94051955 chr13:94051945-94051956 chr13:94051945-94051955
4	FOXA2	chr13:94051760-94052080	HepG2	liver:	n/a	n/a
5	MYC	chr13:94051785-94052096	MCF10A-Er-Src	breast:	n/a	chr13:94051944-94051957 chr13:94051945-94051954 chr13:94051857-94051866 chr13:94051946-94051956 chr13:94051945-94051955 chr13:94051945-94051956 chr13:94051945-94051955
6	FOXA1	chr13:94051748-94052110	HepG2	liver:	n/a	n/a
7	FOS	chr13:94051694-94052024	MCF10A-Er-Src	breast:	n/a	chr13:94051856-94051865 chr13:94051858-94051869 chr13:94051855-94051866
8	MAX	chr13:94051839-94052134	A549	lung:	n/a	chr13:94051944-94051957 chr13:94051945-94051954 chr13:94051857-94051866 chr13:94051946-94051956 chr13:94051945-94051955 chr13:94051945-94051956 chr13:94051945-94051955
9	MAX	chr13:94051772-94052169	MCF-7	breast:	n/a	chr13:94051944-94051957 chr13:94051945-94051954 chr13:94051857-94051866 chr13:94051946-94051956 chr13:94051945-94051955 chr13:94051945-94051956 chr13:94051945-94051955
10	FOXA1	chr13:94051723-94052084	HepG2	liver:	n/a	n/a
11	FOS	chr13:94051744-94051944	MCF10A-Er-Src	breast:	n/a	chr13:94051856-94051865 chr13:94051858-94051869 chr13:94051855-94051866
12	FOSL2	chr13:94051759-94051995	HepG2	liver:	n/a	chr13:94051856-94051865 chr13:94051858-94051869 chr13:94051855-94051866
13	MYC	chr13:94051862-94052042	MCF-7	breast:	n/a	chr13:94051944-94051957 chr13:94051945-94051954 chr13:94051946-94051956 chr13:94051945-94051955 chr13:94051945-94051956 chr13:94051945-94051955
14	FOXA1	chr13:94051726-94052101	HepG2	liver:	n/a	n/a
15	FOXA1	chr13:94051745-94052100	HepG2	liver:	n/a	n/a
16	FOS	chr13:94051728-94052011	MCF10A-Er-Src	breast:	n/a	chr13:94051856-94051865 chr13:94051858-94051869 chr13:94051855-94051866
17	MAX	chr13:94051711-94052230	A549	lung:	n/a	chr13:94051944-94051957 chr13:94051945-94051954 chr13:94051857-94051866 chr13:94051946-94051956 chr13:94051945-94051955 chr13:94051945-94051956 chr13:94051945-94051955
18	FOXA2	chr13:94051658-94052136	A549	lung:	n/a	n/a
19	FOXA2	chr13:94051626-94052103	A549	lung:	n/a	n/a
20	FOS	chr13:94051713-94051983	MCF10A-Er-Src	breast:	n/a	chr13:94051856-94051865 chr13:94051858-94051869 chr13:94051855-94051866

Variant related genes	Relation type
HNRNPA1P29	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11617476	1.00[JPT][hapmap]
rs1323971	0.85[EUR][1000 genomes]
rs1323975	1.00[JPT][hapmap]
rs1323987	0.86[CHB][hapmap]
rs1323988	1.00[JPT][hapmap];0.87[YRI][hapmap]
rs1373835	1.00[JPT][hapmap]
rs1408209	1.00[JPT][hapmap]
rs1408219	1.00[JPT][hapmap]
rs2762095	1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2762097	1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2762100	1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2762104	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2762105	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2762106	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2762107	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2762110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2762111	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2762114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2762116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2762117	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2762119	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2813596	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2813608	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2813609	1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2813610	1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2813615	1.00[JPT][hapmap]
rs4142601	1.00[JPT][hapmap]
rs4771874	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs4773741	1.00[JPT][hapmap]
rs4773742	1.00[JPT][hapmap]
rs66460753	0.85[EUR][1000 genomes]
rs7324202	1.00[JPT][hapmap]
rs7336981	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7338959	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7982827	1.00[JPT][hapmap]
rs7992272	0.81[EUR][1000 genomes]
rs7992679	1.00[JPT][hapmap]
rs8001600	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9301876	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs9524017	1.00[JPT][hapmap]
rs9524021	1.00[JPT][hapmap]
rs9524026	0.85[EUR][1000 genomes]
rs9524027	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs9524068	0.82[EUR][1000 genomes]
rs9561321	1.00[JPT][hapmap]
rs995811	1.00[JPT][hapmap]

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	nsv869070	chr13:93347616-94286933	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1053035	chr13:93842576-94229732	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541880	chr13:93842576-94229732	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv530636	chr13:93997311-94281707	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv916039	chr13:94035909-94191105	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94046600-94052400	Weak transcription	Fetal Brain Male	brain
2	chr13:94047800-94057200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr13:94050600-94052000	Enhancers	A549	lung
4	chr13:94050800-94053000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr13:94051200-94052200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:94051200-94052200	Enhancers	HepG2	liver
7	chr13:94051600-94052200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr13:94051600-94055600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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