Variant report

Variant	rs11580409
Chromosome Location	chr1:75038228-75038229
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:75036442..75039426-chr1:75040101..75042998,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10890134	0.80[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11210479	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11210480	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12067338	0.88[EUR][1000 genomes]
rs12723334	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12728662	0.80[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1443372	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1838131	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2344504	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3845351	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3911349	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4082886	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4650275	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs476332	0.82[JPT][hapmap]
rs484449	0.82[JPT][hapmap]
rs562916	0.82[JPT][hapmap]
rs56710753	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59201609	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6699857	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs686329	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs696692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs696701	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs699848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs699852	0.87[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs699853	0.96[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs699856	0.96[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs699857	0.82[JPT][hapmap]
rs7548647	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	nsv1003171	chr1:74407468-75122270	Strong transcription Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv535000	chr1:74407468-75122270	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv830248	chr1:74962391-75144458	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv870824	chr1:75019390-75125581	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75029800-75044800	Weak transcription	Brain Anterior Caudate	brain
2	chr1:75037200-75038600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:75037400-75038400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
4	chr1:75038000-75038400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:75038000-75038600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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