Variant report

Variant	rs62065425
Chromosome Location	chr17:16828711-16828712
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	chr17:16828602..16830986-chr17:16831048..16832732,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1004439	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11649835	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11650590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11650981	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11651352	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35380019	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55635506	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55770108	0.82[AMR][1000 genomes]
rs56035746	0.82[AMR][1000 genomes]
rs56092540	0.80[AMR][1000 genomes]
rs56369903	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56396775	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56408153	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62065417	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62065418	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62065421	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62065423	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62065424	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62065426	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62065427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62065429	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62065430	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv2753951	chr17:16660721-16848750	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2755100	chr17:16660721-16848750	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv833379	chr17:16683585-16859539	Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1055688	chr17:16800788-16868860	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv960193	chr17:16811200-16831798	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv907726	chr17:16821204-16875636	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv526289	chr17:16821625-16837365	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62065425	LOC96597	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16819800-16831600	Weak transcription	Primary B cells from peripheral blood	blood
2	chr17:16820000-16830800	Weak transcription	GM12878-XiMat	blood
3	chr17:16825200-16831400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr17:16827600-16832400	Weak transcription	Spleen	Spleen
5	chr17:16827800-16829400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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