Variant report

Variant	rs12540446
Chromosome Location	chr7:11605996-11605997
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	chr7:11605955..11606651-chr7:11870687..11871656,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1034739	0.81[EUR][1000 genomes]
rs1034741	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12540394	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12699203	0.87[CEU][hapmap]
rs17635562	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2023864	0.87[MEX][hapmap]
rs2051796	0.82[AMR][1000 genomes]
rs2107143	0.95[JPT][hapmap]
rs2107479	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214586	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs28478051	0.83[EUR][1000 genomes]
rs30	0.89[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs37	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs38	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs53	0.89[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs6963353	0.83[MEX][hapmap]
rs6979362	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72	0.83[ASN][1000 genomes]
rs73	0.90[CHB][hapmap];0.96[CHD][hapmap];0.86[ASN][1000 genomes]
rs74	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs75	0.90[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs77	0.90[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs7784891	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs78	0.90[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs7801339	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7801865	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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	nsv1028326	chr7:11221209-11754436	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv538733	chr7:11221209-11754436	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1023665	chr7:11457493-11773517	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv887606	chr7:11473561-11771288	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv606199	chr7:11506143-12486659	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:11577400-11615200	Weak transcription	Placenta	Placenta
2	chr7:11602800-11606800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:11605400-11606000	Enhancers	Liver	Liver
4	chr7:11605400-11606200	Enhancers	A549	lung

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