Variant report

Variant	rs5675
Chromosome Location	chr1:71477539-71477540
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	chr1:71475910..71477737-chr1:71480653..71482581,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11209732	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11209742	0.86[ASN][1000 genomes]
rs12035634	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12037493	0.80[AMR][1000 genomes]
rs12039343	0.81[EUR][1000 genomes]
rs12405786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12409424	0.80[AMR][1000 genomes]
rs1409164	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17090778	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1883460	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2206343	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2223501	0.80[ASN][1000 genomes]
rs2256385	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2268052	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2284361	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2284363	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2300162	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2300165	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2300168	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2300176	1.00[ASN][1000 genomes]
rs2300177	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35316490	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3819787	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4649933	1.00[ASN][1000 genomes]
rs4649934	0.80[AMR][1000 genomes]
rs484538	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs5024204	0.92[ASN][1000 genomes]
rs55669216	0.81[EUR][1000 genomes]
rs570021	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs6424414	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs646511	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs646621	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs66539808	0.90[ASN][1000 genomes]
rs6678886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66904764	0.90[ASN][1000 genomes]
rs6698339	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7531139	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7534885	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7537324	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs909848	0.86[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1845198	chr1:71274759-71514969	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv830148	chr1:71310366-71483932	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv871313	chr1:71391646-71489438	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1008902	chr1:71417926-71488139	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv534989	chr1:71417926-71488139	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv546472	chr1:71432984-71541003	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	555 gene(s)	inside rSNPs	diseases
7	nsv461851	chr1:71442626-71507541	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
8	nsv546473	chr1:71442626-71507541	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
9	esv1850593	chr1:71444149-71514969	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active 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
10	nsv870843	chr1:71465292-71489438	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
11	nsv870734	chr1:71469583-71485036	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
12	nsv870576	chr1:71469583-71489438	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71465800-71485000	Weak transcription	Pancreas	Pancrea
2	chr1:71470600-71477600	Weak transcription	Adipose Nuclei	Adipose
3	chr1:71473600-71478000	Weak transcription	Aorta	Aorta
4	chr1:71474600-71478200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:71475400-71478200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:71477200-71478600	Strong transcription	K562	blood

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