Variant report

Variant	rs1984703
Chromosome Location	chr5:178122284-178122285
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	chr5:178119500..178121494-chr5:178122164..178124985,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1000057	0.99[ASN][1000 genomes]
rs10042073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10058283	0.82[EUR][1000 genomes]
rs10072060	0.92[ASN][1000 genomes]
rs12518753	0.92[ASN][1000 genomes]
rs1585686	0.82[EUR][1000 genomes]
rs2078257	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2169762	0.81[EUR][1000 genomes]
rs2335443	0.82[EUR][1000 genomes]
rs3927097	0.92[ASN][1000 genomes]
rs4246821	0.90[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6600943	0.89[EUR][1000 genomes]
rs6866344	0.82[EUR][1000 genomes]
rs6898275	0.88[ASN][1000 genomes]
rs7704813	0.87[ASN][1000 genomes]
rs7711731	0.92[ASN][1000 genomes]
rs7715476	0.99[ASN][1000 genomes]
rs7719405	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7736628	0.86[ASN][1000 genomes]
rs931056	0.99[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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1023697	chr5:178070594-178126328	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv537972	chr5:178070594-178126328	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv5155	chr5:178075100-178132799	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv883217	chr5:178099758-178193081	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv1837537	chr5:178103405-178122284	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	esv1840322	chr5:178103405-178122284	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	esv1844379	chr5:178111284-178122284	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1984703	CLK4	cis	Whole Blood	GTEx
rs1984703	ZNF354A	cis	Whole Blood	GTEx
rs1984703	FAM193B	cis	parietal	SCAN
rs1984703	TMED9	cis	parietal	SCAN
rs1984703	ZNF354A	cis	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178122000-178123000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:178122000-178123200	Enhancers	Primary neutrophils fromperipheralblood	blood

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