Variant report

Variant	rs34546531
Chromosome Location	chr15:62363300-62363301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:62357601..62360686-chr15:62360802..62364205,4	MCF-7	breast:
2	chr15:62352114..62355489-chr15:62359291..62363476,4	MCF-7	breast:
3	chr15:62361138..62363897-chr15:62365785..62367372,2	MCF-7	breast:
4	chr15:62363137..62365587-chr15:62379129..62382052,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259251	Chromatin interaction
ENSG00000198535	Chromatin interaction
ENSG00000129003	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10519155	1.00[ASN][1000 genomes]
rs10519156	1.00[ASN][1000 genomes]
rs11629645	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11632560	1.00[AFR][1000 genomes]
rs11633932	1.00[ASN][1000 genomes]
rs11634077	0.88[EUR][1000 genomes]
rs11634306	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11634312	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11634818	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636682	1.00[ASN][1000 genomes]
rs11637599	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11637693	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11639286	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12148573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12905264	0.80[EUR][1000 genomes]
rs12909386	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12909673	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12911068	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911422	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12913358	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12916410	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12917339	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12917444	1.00[ASN][1000 genomes]
rs17271312	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17271389	1.00[ASN][1000 genomes]
rs34017665	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34042779	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34088392	0.83[AMR][1000 genomes]
rs34173668	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34282385	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34311301	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34338090	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34391931	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34933463	0.83[EUR][1000 genomes]
rs34958705	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35119291	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35168171	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35324423	0.83[AMR][1000 genomes]
rs35577653	1.00[ASN][1000 genomes]
rs35785804	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35932993	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36126734	0.83[AMR][1000 genomes]
rs36175042	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4143844	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4143845	0.89[AMR][1000 genomes]
rs62006969	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62007448	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62007453	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007454	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007455	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62007767	1.00[ASN][1000 genomes]
rs62008531	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62008549	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457176	chr15:62178695-62519658	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv569643	chr15:62178695-62519658	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv471247	chr15:62202481-62519658	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv569646	chr15:62202482-62519658	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv1044748	chr15:62276183-62521856	Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv542405	chr15:62276183-62521856	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv457178	chr15:62340126-62394324	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv569652	chr15:62340126-62394324	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv1560	chr15:62354264-62399304	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34546531	VPS13C	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62361600-62367400	Weak transcription	Hela-S3	cervix

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