Variant report

Variant	rs13398962
Chromosome Location	chr2:142835731-142835732
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:142832252..142835067-chr2:142835097..142836717,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1001628	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1011861	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10179879	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10181071	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10190320	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10201480	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10205169	1.00[JPT][hapmap]
rs11677303	0.94[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12691633	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12994651	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13012748	0.80[ASN][1000 genomes]
rs13385180	1.00[YRI][hapmap]
rs13400121	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13401617	1.00[ASN][1000 genomes]
rs13405280	1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13408764	1.00[ASN][1000 genomes]
rs13412878	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs13418304	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13420312	1.00[JPT][hapmap]
rs1375607	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449502	0.80[ASN][1000 genomes]
rs1562704	1.00[MEX][hapmap]
rs1562705	0.94[CEU][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16847971	0.80[ASN][1000 genomes]
rs1982384	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2044731	1.00[CHB][hapmap]
rs34199884	1.00[ASN][1000 genomes]
rs34725547	0.80[ASN][1000 genomes]
rs35975765	1.00[ASN][1000 genomes]
rs4267463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62155635	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6749591	1.00[YRI][hapmap]
rs7574284	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7583748	1.00[MEX][hapmap]
rs895935	0.94[CEU][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs956799	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs956800	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9630925	1.00[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	nsv530398	chr2:142474842-142843839	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv997274	chr2:142760393-143599193	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv526107	chr2:142768518-142884248	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv875253	chr2:142805006-142855291	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv875254	chr2:142833327-142931146	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142829400-142838200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:142835400-142836000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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