Variant report

Variant	rs13172426
Chromosome Location	chr5:49883983-49883984
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	chr5:49882674..49884929-chr5:49963265..49965017,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151883	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13155662	0.83[AMR][1000 genomes]
rs13157952	0.84[EUR][1000 genomes]
rs13159553	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13162663	0.82[EUR][1000 genomes]
rs13167408	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13169200	0.89[EUR][1000 genomes]
rs13171248	0.84[EUR][1000 genomes]
rs13172836	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13176737	0.83[AMR][1000 genomes]
rs13180485	0.98[EUR][1000 genomes]
rs13180506	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13183686	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1968637	0.84[EUR][1000 genomes]
rs2354531	0.84[EUR][1000 genomes]
rs34183555	0.83[AMR][1000 genomes]
rs34443769	0.98[EUR][1000 genomes]
rs35210389	0.82[EUR][1000 genomes]
rs35292338	0.89[EUR][1000 genomes]
rs35434227	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35596019	0.89[EUR][1000 genomes]
rs36187734	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6892149	0.82[EUR][1000 genomes]
rs71615974	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71615975	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71631479	0.98[EUR][1000 genomes]
rs71631481	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7723395	0.84[EUR][1000 genomes]
rs7730188	0.98[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	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv964850	chr5:49883635-49942856	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13172426	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49876800-49891400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:49877400-49884000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:49881800-49884600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr5:49882600-49884000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:49883800-49884200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:49883800-49884800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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