Variant report

Variant	rs461259
Chromosome Location	chr5:177002089-177002090
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:176983331..176986206-chr5:177001141..177003444,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11537644	0.86[ASN][1000 genomes]
rs12515554	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs13169820	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs13175194	0.87[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap]
rs13175367	0.88[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap]
rs189243	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28499263	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28587776	0.87[ASN][1000 genomes]
rs28693973	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28712028	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2878523	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs335485	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs337341	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs337362	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34582406	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34857879	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs364970	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs366470	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs461163	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7718106	0.84[ASN][1000 genomes]
rs834549	0.89[EUR][1000 genomes];0.90[ASN][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	nsv916108	chr5:176688459-177078723	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
3	nsv883164	chr5:176780545-177003616	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv883177	chr5:176868358-177003616	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
6	nsv1022630	chr5:176975746-177028082	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv537966	chr5:176975746-177028082	Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv883181	chr5:176978496-177034786	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv883182	chr5:176980995-177322056	Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	esv3348457	chr5:176995395-177020808	Active TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs461259	FAM153C	cis	Esophagus Muscularis	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177001600-177003400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:177001600-177003600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr5:177001600-177003600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:177001800-177003000	Enhancers	H9 Cell Line	embryonic stem cell
5	chr5:177001800-177003000	Enhancers	Esophagus	oesophagus
6	chr5:177001800-177003600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:177001800-177003600	Enhancers	HMEC	breast
8	chr5:177001800-177003600	Enhancers	NHEK	skin
9	chr5:177002000-177002800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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