Variant report

Variant	rs4714870
Chromosome Location	chr6:12797055-12797056
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:12795558..12798232-chr6:12799651..12801381,3	MCF-7	breast:

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10948235	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10948247	1.00[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[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753864	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758650	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][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]
rs12524974	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528956	1.00[CHB][hapmap]
rs12530186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196135	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13203774	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13203883	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214313	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13217579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332840	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1332841	1.00[CHB][hapmap]
rs1360579	1.00[CHB][hapmap]
rs1412738	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1412740	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1412741	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1412744	1.00[CHB][hapmap]
rs1412749	1.00[ASN][1000 genomes]
rs1412751	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs1412752	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572000	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1572002	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs16873383	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17617207	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs17679417	1.00[CHB][hapmap]
rs17679501	1.00[CHB][hapmap]
rs1953089	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015764	1.00[ASN][1000 genomes]
rs2095123	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327616	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327617	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2327619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28451666	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34498965	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711841	0.93[ASN][1000 genomes]
rs4711857	1.00[CHB][hapmap]
rs4711858	1.00[CHB][hapmap]
rs4714866	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4714868	1.00[ASN][1000 genomes]
rs4714946	1.00[CHB][hapmap]
rs6458460	1.00[ASN][1000 genomes]
rs6458461	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6458473	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458503	1.00[CHB][hapmap]
rs6909834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913075	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916397	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6916418	1.00[ASN][1000 genomes]
rs6916421	1.00[ASN][1000 genomes]
rs6917493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6919327	1.00[ASN][1000 genomes]
rs6922482	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6922969	1.00[ASN][1000 genomes]
rs6924150	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6930873	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935309	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938417	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs6941422	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs6941624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7747656	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748950	1.00[CHB][hapmap]
rs7757205	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7757835	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757858	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs7758513	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760286	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762417	1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762547	1.00[ASN][1000 genomes]
rs7764490	1.00[ASN][1000 genomes]
rs7770745	1.00[CHB][hapmap]
rs7771962	1.00[CHB][hapmap]
rs7776079	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs883947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296465	1.00[ASN][1000 genomes]
rs9296494	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[TSI][hapmap]
rs9381391	1.00[ASN][1000 genomes]
rs9395190	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs944766	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs944767	1.00[CHB][hapmap]
rs9463106	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9463110	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs9463134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463136	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463137	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463138	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472551	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs9472558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9472587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472590	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472594	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472595	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472777	1.00[CHB][hapmap]
rs9472786	1.00[CHB][hapmap]
rs950720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv830587	chr6:12769661-12939875	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv830588	chr6:12793530-12972493	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4714870	TFAP2A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12791200-12797800	Weak transcription	Fetal Brain Female	brain
2	chr6:12793400-12801400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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