Variant report

Variant	rs11951076
Chromosome Location	chr5:60420211-60420212
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	chr5:60417821..60420681-chr5:60456901..60458465,2	MCF-7	breast:
2	chr5:60412981..60415103-chr5:60419112..60420959,2	K562	blood:

Variant related genes	Relation type
ENSG00000251279	Chromatin interaction
ENSG00000188725	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10939881	0.83[AFR][1000 genomes]
rs10939882	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957772	0.87[EUR][1000 genomes]
rs124898	0.86[EUR][1000 genomes]
rs12518792	0.85[AFR][1000 genomes]
rs12518865	0.87[EUR][1000 genomes]
rs13168191	0.87[EUR][1000 genomes]
rs13171576	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382914	0.81[EUR][1000 genomes]
rs1526896	0.83[AFR][1000 genomes]
rs158564	0.82[EUR][1000 genomes]
rs158923	0.81[EUR][1000 genomes]
rs158924	0.81[EUR][1000 genomes]
rs159358	0.86[EUR][1000 genomes]
rs159376	0.85[EUR][1000 genomes]
rs159377	0.88[EUR][1000 genomes]
rs159378	0.88[EUR][1000 genomes]
rs159380	0.88[EUR][1000 genomes]
rs159537	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162234	0.82[EUR][1000 genomes]
rs162238	0.81[EUR][1000 genomes]
rs162241	0.81[EUR][1000 genomes]
rs162242	0.82[EUR][1000 genomes]
rs162244	0.81[EUR][1000 genomes]
rs162247	0.80[EUR][1000 genomes]
rs172348	0.81[EUR][1000 genomes]
rs172945	0.81[EUR][1000 genomes]
rs182410	0.86[EUR][1000 genomes]
rs185354	0.81[EUR][1000 genomes]
rs187459	0.85[EUR][1000 genomes]
rs1983484	0.81[AFR][1000 genomes]
rs2049579	0.81[AFR][1000 genomes]
rs2080869	0.87[EUR][1000 genomes]
rs2112365	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263514	0.81[EUR][1000 genomes]
rs248677	0.82[EUR][1000 genomes]
rs248682	0.87[EUR][1000 genomes]
rs248685	0.87[EUR][1000 genomes]
rs2545475	0.87[EUR][1000 genomes]
rs2545478	0.87[EUR][1000 genomes]
rs2545503	0.85[EUR][1000 genomes]
rs2650512	0.81[EUR][1000 genomes]
rs2650517	0.81[EUR][1000 genomes]
rs2694530	0.81[EUR][1000 genomes]
rs2694531	0.81[EUR][1000 genomes]
rs290503	0.81[EUR][1000 genomes]
rs290506	0.81[EUR][1000 genomes]
rs290507	0.81[EUR][1000 genomes]
rs2950235	0.81[EUR][1000 genomes]
rs295522	0.86[EUR][1000 genomes]
rs295532	0.84[EUR][1000 genomes]
rs295533	0.87[EUR][1000 genomes]
rs295551	0.87[EUR][1000 genomes]
rs295560	0.86[EUR][1000 genomes]
rs295566	0.87[EUR][1000 genomes]
rs295569	0.88[EUR][1000 genomes]
rs295579	0.88[EUR][1000 genomes]
rs298629	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108388	0.81[EUR][1000 genomes]
rs329622	0.81[EUR][1000 genomes]
rs329623	0.81[EUR][1000 genomes]
rs329625	0.81[EUR][1000 genomes]
rs329626	0.80[EUR][1000 genomes]
rs34593	0.82[EUR][1000 genomes]
rs34609	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34613	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34614	0.86[EUR][1000 genomes]
rs34616	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34617	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34621	0.86[EUR][1000 genomes]
rs34624	0.87[EUR][1000 genomes]
rs34625	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34636	0.88[EUR][1000 genomes]
rs34637	0.88[EUR][1000 genomes]
rs34639	0.85[EUR][1000 genomes]
rs34644	0.85[EUR][1000 genomes]
rs39661	0.88[EUR][1000 genomes]
rs40084	0.85[EUR][1000 genomes]
rs4141502	0.87[EUR][1000 genomes]
rs4699969	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56159106	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56409036	0.81[EUR][1000 genomes]
rs6878124	0.87[EUR][1000 genomes]
rs6886481	0.87[EUR][1000 genomes]
rs723276	0.87[EUR][1000 genomes]
rs72759215	0.83[AFR][1000 genomes]
rs7701839	0.86[EUR][1000 genomes]
rs7706753	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7713481	0.84[AFR][1000 genomes]
rs7721096	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7734205	0.83[AFR][1000 genomes]
rs7737276	0.87[AFR][1000 genomes]
rs810883	0.87[EUR][1000 genomes]
rs888799	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv869065	chr5:60180775-60428760	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv598314	chr5:60374912-60459040	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11951076	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs11951076	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60395400-60428200	Weak transcription	HSMMtube	muscle
2	chr5:60396800-60420400	Weak transcription	Ovary	ovary
3	chr5:60398800-60453800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:60402800-60420600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr5:60411200-60420600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:60411200-60422400	Weak transcription	Aorta	Aorta
7	chr5:60415600-60421800	Weak transcription	Esophagus	oesophagus
8	chr5:60417200-60449400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr5:60420000-60423200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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