Variant report

Variant	rs2725854
Chromosome Location	chr15:56577831-56577832
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	chr15:56534615..56536116-chr15:56577645..56579684,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181827	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11630363	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs11633374	0.81[EUR][1000 genomes]
rs11855094	0.91[CHB][hapmap]
rs12900678	0.86[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12905782	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap]
rs12905899	0.96[CEU][hapmap];0.87[YRI][hapmap]
rs12911094	0.96[CEU][hapmap];0.84[MKK][hapmap];0.88[YRI][hapmap]
rs12911427	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs1372753	0.96[CEU][hapmap]
rs1402177	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1477590	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1549452	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs16976890	0.91[CHB][hapmap]
rs17819438	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes]
rs2114183	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2119937	0.96[CEU][hapmap];0.88[YRI][hapmap]
rs2249090	0.88[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2303441	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs2460646	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2460648	0.81[AMR][1000 genomes]
rs2460650	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2465973	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554287	0.91[CHB][hapmap]
rs2682012	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2682019	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2682021	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2682023	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2682044	0.81[AMR][1000 genomes]
rs2682049	0.83[AMR][1000 genomes]
rs2682051	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2682053	0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2682054	0.96[CEU][hapmap];0.82[AMR][1000 genomes]
rs2682059	0.96[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs2713924	0.96[CEU][hapmap]
rs2713931	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2713933	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2713936	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2713941	0.96[CEU][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes]
rs2718901	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2718908	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2718921	0.91[CHB][hapmap]
rs2718934	0.96[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs2718941	0.96[CEU][hapmap];0.88[YRI][hapmap]
rs2725856	0.82[CHB][hapmap]
rs2725862	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2725870	0.81[AMR][1000 genomes]
rs2947020	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2947021	0.88[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35497167	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35863560	0.84[EUR][1000 genomes]
rs3784552	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs3817406	0.92[CEU][hapmap];0.95[CHB][hapmap]
rs3985758	0.84[EUR][1000 genomes]
rs4310791	0.96[CEU][hapmap];0.80[TSI][hapmap]
rs4310792	0.96[CEU][hapmap]
rs4774232	0.96[CEU][hapmap]
rs62022122	0.84[EUR][1000 genomes]
rs6493856	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs6493858	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap]
rs7170307	0.85[CEU][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs7181235	0.91[CHB][hapmap]
rs7181320	0.85[CEU][hapmap]
rs7496025	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.88[YRI][hapmap]
rs795791	0.86[CHB][hapmap]
rs795800	0.91[CHB][hapmap]
rs8024031	0.96[CEU][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];0.88[YRI][hapmap]
rs9672886	0.92[CEU][hapmap];0.87[YRI][hapmap]
rs9672928	0.85[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2725854	RFX7	cis	Skin Sun Exposed Lower leg	GTEx
rs2725854	FLJ12994	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56577400-56579000	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr15:56577600-56578600	Weak transcription	Placenta	Placenta

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