Variant report

Variant	rs7516705
Chromosome Location	chr1:216055286-216055287
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	chr1:216055217-216055294	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000229242	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10779661	0.81[CHB][hapmap]
rs10864207	0.81[CHB][hapmap];0.80[CHD][hapmap];0.80[JPT][hapmap]
rs10864208	0.81[CHB][hapmap];0.83[CHD][hapmap];0.80[JPT][hapmap]
rs11120653	0.81[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs11120666	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs11120684	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11526532	0.81[CHB][hapmap]
rs12021707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs12037661	0.87[CHB][hapmap]
rs12567496	0.82[CEU][hapmap]
rs1547765	0.85[JPT][hapmap]
rs1934425	0.82[AMR][1000 genomes]
rs1934429	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2027355	0.81[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap]
rs3884585	0.81[CHB][hapmap]
rs4363405	0.80[CHD][hapmap]
rs4390149	0.80[CHD][hapmap]
rs4405115	0.81[CHB][hapmap]
rs4528090	0.81[CHB][hapmap]
rs6540912	0.80[CHD][hapmap]
rs6701765	0.81[CHB][hapmap];0.80[CHD][hapmap]
rs721099	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs975994	0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap]
rs9887827	0.80[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430324	chr1:215649163-216082605	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1006504	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv535288	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv949671	chr1:215942740-216120815	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv832548	chr1:215987089-216175724	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv468127	chr1:216054086-216066437	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv549193	chr1:216054086-216066437	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7516705	PROX1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216055200-216055400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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