Variant report

Variant	rs1654545
Chromosome Location	chr19:51435852-51435853
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:51432732..51437222-chr19:51477627..51480793,4	MCF-7	breast:
2	chr19:51434633..51437276-chr19:51470056..51473720,4	MCF-7	breast:
3	chr19:51435279..51436842-chr19:51510358..51513256,2	MCF-7	breast:
4	chr19:51427739..51428732-chr19:51435714..51436347,2	K562	blood:
5	chr19:51409507..51410240-chr19:51435323..51436234,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167755	Chromatin interaction
ENSG00000167749	Chromatin interaction
ENSG00000267879	Chromatin interaction
ENSG00000213022	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10402016	0.85[CEU][hapmap]
rs10408037	0.93[EUR][1000 genomes]
rs10408594	0.93[EUR][1000 genomes]
rs10408900	0.93[EUR][1000 genomes]
rs10410662	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10410677	0.96[EUR][1000 genomes]
rs10420829	0.94[EUR][1000 genomes]
rs1701906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1701907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1701908	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1701909	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1701911	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1865068	0.96[EUR][1000 genomes]
rs2659083	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2659084	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59178825	0.93[EUR][1000 genomes]
rs59753071	0.94[EUR][1000 genomes]
rs7246283	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes]
rs7246770	0.97[EUR][1000 genomes]
rs7251270	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs7252452	0.94[EUR][1000 genomes]
rs7255117	0.94[EUR][1000 genomes]
rs7255259	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51432800-51437400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:51433200-51437600	Enhancers	HMEC	breast
3	chr19:51434000-51453200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:51435000-51436000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr19:51435200-51436000	Enhancers	A549	lung
6	chr19:51435400-51436200	Flanking Active TSS	NHEK	skin
7	chr19:51435600-51436000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr19:51435600-51436000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:51435600-51436800	Weak transcription	Hela-S3	cervix
10	chr19:51435600-51439000	Weak transcription	Esophagus	oesophagus

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