Variant report

Variant	rs16865647
Chromosome Location	chr2:178561428-178561429
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	chr2:178561087-178561508	HepG2	liver:	n/a	chr2:178561358-178561370

No.	Distal block	Cell Line	Cell type
1	chr2:178554622..178556769-chr2:178559553..178561777,2	K562	blood:
2	chr2:178561207..178563093-chr2:178570078..178571660,2	MCF-7	breast:
3	chr2:178559293..178562880-chr2:178620510..178622541,4	K562	blood:

Variant related genes	Relation type
ENSG00000229941	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10497487	1.00[YRI][hapmap]
rs10497490	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs10497491	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs1561316	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs1561317	0.87[YRI][hapmap];0.87[AFR][1000 genomes]
rs16865617	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16865625	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16865641	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16865642	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16865643	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16865645	0.84[YRI][hapmap]
rs16865651	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16865668	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs16865670	0.87[AFR][1000 genomes]
rs16865676	0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs16865678	0.83[YRI][hapmap]
rs16865684	0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs16865689	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs16865694	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs16865697	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs16865703	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs16865711	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs16865753	0.83[YRI][hapmap]
rs16865776	0.91[YRI][hapmap]
rs4464320	0.87[AFR][1000 genomes]
rs4541282	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs4585066	0.86[YRI][hapmap];0.87[AFR][1000 genomes]
rs73028304	1.00[AMR][1000 genomes]
rs934808	0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs934810	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv431812	chr2:178525371-178584470	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1007925	chr2:178535922-178577002	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv870023	chr2:178545623-178581407	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1005854	chr2:178546907-178586608	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv2762967	chr2:178546919-178577002	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1005991	chr2:178550049-178577002	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv528219	chr2:178551924-178567151	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1003983	chr2:178551958-178577002	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 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	chr2:178558200-178576600	Weak transcription	Pancreas	Pancrea
2	chr2:178558600-178562000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:178559000-178563600	Weak transcription	Ovary	ovary
4	chr2:178559200-178561600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:178559800-178561600	Weak transcription	Fetal Kidney	kidney
6	chr2:178560800-178562000	Enhancers	HepG2	liver
7	chr2:178561200-178562200	Enhancers	Liver	Liver

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