Variant report

Variant	rs12616932
Chromosome Location	chr2:212824999-212825000
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:212819022..212821702-chr2:212822393..212825012,4	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10205607	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs10497957	0.94[YRI][hapmap]
rs12473131	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap]
rs12623434	0.82[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.81[MEX][hapmap]
rs1402719	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs16847357	0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs2083297	0.91[ASW][hapmap];0.81[LWK][hapmap];0.89[YRI][hapmap]
rs2685006	0.99[ASN][1000 genomes]
rs2888037	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs34306926	0.85[AFR][1000 genomes]
rs4673644	0.82[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap]
rs6435682	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs6707590	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6744796	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs67565187	0.85[AFR][1000 genomes]
rs707284	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs72935738	0.94[ASN][1000 genomes]
rs839499	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs839500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs839501	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs839504	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs839512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs839515	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs839516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs839517	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.99[ASN][1000 genomes]
rs839518	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs839519	0.86[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs839520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs839521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs839522	0.99[ASN][1000 genomes]
rs839523	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.99[ASN][1000 genomes]
rs839540	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs839541	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs860821	0.95[ASN][1000 genomes]
rs864528	0.99[ASN][1000 genomes]
rs990741	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34128	chr2:212581485-212857122	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv834525	chr2:212693190-212860356	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv875791	chr2:212824999-212874828	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv875792	chr2:212824999-212896571	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12616932	RPE	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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