Variant report

Variant	rs13088225
Chromosome Location	chr3:146164274-146164275
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	chr3:146158889..146161569-chr3:146161974..146164517,2	MCF-7	breast:

Extended variants
information (count: 131 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10804713	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10804714	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10935626	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10935631	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935632	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11720256	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12053987	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12054302	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12054308	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12054453	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12054455	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12107218	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12486656	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12486737	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12487546	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs12487572	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12492503	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12494007	0.86[CEU][hapmap];0.94[CHB][hapmap]
rs12494206	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12497907	0.83[EUR][1000 genomes]
rs12629356	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12629420	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12633694	0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[ASN][1000 genomes]
rs13064298	0.83[EUR][1000 genomes]
rs13068178	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068800	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13081634	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13090489	0.84[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13092702	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1403640	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1403641	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403642	0.95[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403643	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1403644	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1403645	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523334	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1523335	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1523336	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1608389	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1608390	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1608391	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap]
rs1608392	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17351881	0.95[CHB][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2037565	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2091064	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2222465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2222466	0.81[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2868436	0.81[CEU][hapmap];0.95[CHB][hapmap]
rs2868438	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34198003	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34359311	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34535967	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34696856	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34740686	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35082616	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35223042	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35336826	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35374128	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35695439	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4234358	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4282029	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4333063	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4334615	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4355250	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4380387	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4389447	0.83[EUR][1000 genomes]
rs4444684	0.81[CEU][hapmap];0.94[CHB][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4476473	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4558726	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4569626	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4572737	0.84[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4597678	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4600794	0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[ASN][1000 genomes]
rs4681119	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4681120	0.88[CEU][hapmap];0.94[CHB][hapmap]
rs4681318	0.84[EUR][1000 genomes]
rs4681319	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4681320	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4681321	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4681322	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4681326	0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs473517	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs506791	0.89[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs509382	0.85[ASN][1000 genomes]
rs533756	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs535344	0.98[ASN][1000 genomes]
rs544043	0.85[ASN][1000 genomes]
rs544979	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs570781	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs574318	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs57545585	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58445343	0.82[EUR][1000 genomes]
rs6440429	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6440430	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6440432	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6440435	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6766583	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6766800	0.81[CEU][hapmap];0.95[CHB][hapmap]
rs6767156	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs6770000	0.83[EUR][1000 genomes]
rs6774338	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6794891	0.83[EUR][1000 genomes]
rs6794893	0.83[EUR][1000 genomes]
rs6798352	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6801846	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6801964	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6806369	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6806535	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap]
rs692749	0.85[ASN][1000 genomes]
rs7431927	0.83[EUR][1000 genomes]
rs7434147	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7434212	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7614557	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7617214	0.89[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7619521	0.83[EUR][1000 genomes]
rs7620107	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7628445	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7633474	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7645939	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646988	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7650361	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7650546	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7653701	1.00[ASW][hapmap];0.89[CEU][hapmap];0.89[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940193	0.81[CEU][hapmap];0.95[CHB][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs955611	0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877617	chr3:146096182-146172109	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv877618	chr3:146096182-146192324	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv877619	chr3:146106142-146172109	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
4	nsv877620	chr3:146109354-146172109	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
5	nsv877621	chr3:146117041-146172109	Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
6	nsv877622	chr3:146131961-146219740	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr3:146164000-146164400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:146164000-146164600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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