Variant report

Variant	rs7329539
Chromosome Location	chr13:94052090-94052091
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	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
3	FOXA1	chr13:94051748-94052110	HepG2	liver:	n/a	n/a
4	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
5	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
6	FOXA1	chr13:94051726-94052101	HepG2	liver:	n/a	n/a
7	FOXA1	chr13:94051745-94052100	HepG2	liver:	n/a	n/a
8	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
9	FOXA2	chr13:94051658-94052136	A549	lung:	n/a	n/a
10	FOXA2	chr13:94051626-94052103	A549	lung:	n/a	n/a

Variant related genes	Relation type
HNRNPA1P29	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1323972	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1323989	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1359198	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1408211	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1445266	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1445275	0.86[EUR][1000 genomes]
rs17234460	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17300206	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1924383	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1947077	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1980727	0.91[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.90[EUR][1000 genomes]
rs2025947	1.00[CEU][hapmap]
rs2038727	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2590549	0.81[CHB][hapmap]
rs2762082	0.91[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2762092	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2762120	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2813627	0.81[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs3814277	1.00[CEU][hapmap]
rs4771875	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4773744	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4773745	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4773746	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4773747	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72640517	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7338402	0.91[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7994277	1.00[CEU][hapmap]
rs7997302	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8002366	1.00[CEU][hapmap]
rs876808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs895193	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9301877	1.00[CEU][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9301881	0.86[JPT][hapmap]
rs9516225	1.00[CEU][hapmap]
rs9516228	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9524029	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524038	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9524039	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9524045	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9524047	0.88[ASN][1000 genomes]
rs9524051	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9524053	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9524058	0.90[EUR][1000 genomes]
rs9524061	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9524070	0.91[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs9524075	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9556289	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9556291	0.86[EUR][1000 genomes]
rs9561315	1.00[CEU][hapmap]
rs9561322	1.00[CEU][hapmap]
rs9561326	1.00[CEU][hapmap]
rs9561329	1.00[CEU][hapmap]
rs9561334	0.86[CEU][hapmap]
rs9561336	1.00[CEU][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9561340	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9561346	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9561347	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs973302	0.91[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs974542	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs996460	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs996461	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs996463	0.81[CHB][hapmap];0.86[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:7 , 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	chr13:94050800-94053000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr13:94051200-94052200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:94051200-94052200	Enhancers	HepG2	liver
6	chr13:94051600-94052200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr13:94051600-94055600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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