Variant report

Variant	rs6499978
Chromosome Location	chr16:58807766-58807767
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	FOXA1	chr16:58807629-58808245	HepG2	liver:	n/a	n/a
2	TEAD4	chr16:58807745-58808176	HepG2	liver:	n/a	n/a
3	FOXA1	chr16:58807646-58808204	HepG2	liver:	n/a	n/a
4	SP1	chr16:58807716-58808107	HepG2	liver:	n/a	n/a
5	EP300	chr16:58807726-58808089	HepG2	liver:	n/a	n/a
6	FOXA1	chr16:58807766-58808240	HepG2	liver:	n/a	n/a
7	NFIC	chr16:58807693-58808221	HepG2	liver:	n/a	n/a
8	FOXA2	chr16:58807266-58808411	HepG2	liver:	n/a	n/a
9	NR2F2	chr16:58807644-58808249	HepG2	liver:	n/a	n/a
10	FOXA1	chr16:58807766-58808063	A549	lung:	n/a	n/a
11	HDAC2	chr16:58807745-58808111	HepG2	liver:	n/a	n/a
12	ARID3A	chr16:58807562-58808192	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
GEMIN8P2	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11643711	0.85[ASN][1000 genomes]
rs11644269	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs11859128	0.85[ASN][1000 genomes]
rs12709011	0.89[ASN][1000 genomes]
rs12919151	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12925419	0.85[ASN][1000 genomes]
rs12925537	0.85[ASN][1000 genomes]
rs12931903	0.83[ASN][1000 genomes]
rs1898234	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2013333	0.85[ASN][1000 genomes]
rs28579863	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34295929	0.83[ASN][1000 genomes]
rs4784054	0.84[ASN][1000 genomes]
rs4784980	0.89[ASN][1000 genomes]
rs6499977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186453	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7206052	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs73553527	0.89[ASN][1000 genomes]
rs8044439	0.85[ASN][1000 genomes]
rs8044904	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8045828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046937	0.89[ASN][1000 genomes]
rs8047097	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8047394	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8052646	0.85[ASN][1000 genomes]
rs8052824	0.89[ASN][1000 genomes]
rs8054775	0.88[ASN][1000 genomes]
rs8059778	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9937890	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	esv2758427	chr16:58579005-58876037	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2758650	chr16:58579005-58876037	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1065296	chr16:58738198-58837859	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	n/a
4	nsv1065269	chr16:58743487-58972224	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv520998	chr16:58807542-58834219	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58806600-58808400	Enhancers	Liver	Liver
2	chr16:58807600-58808600	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links