Variant report

Variant	rs7715476
Chromosome Location	chr5:178120334-178120335
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1000057	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10042073	0.99[ASN][1000 genomes]
rs10072060	0.92[ASN][1000 genomes]
rs12518753	0.92[ASN][1000 genomes]
rs1984703	0.99[ASN][1000 genomes]
rs2078257	0.99[ASN][1000 genomes]
rs3927097	0.92[ASN][1000 genomes]
rs4246821	0.90[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6898275	0.88[ASN][1000 genomes]
rs7704813	0.87[ASN][1000 genomes]
rs7711731	0.92[ASN][1000 genomes]
rs7719405	0.80[ASN][1000 genomes]
rs7736628	0.86[ASN][1000 genomes]
rs931056	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv600437	chr5:178111284-178120334	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv1844379	chr5:178111284-178122284	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv600446	chr5:178111743-178120334	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv600451	chr5:178112451-178120334	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv3471131	chr5:178116546-178121044	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv3471132	chr5:178116546-178121044	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv3410880	chr5:178117146-178120544	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv3329723	chr5:178117596-178120394	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7715476	PDLIM7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178118000-178122000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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