Variant report

Variant	rs13397728
Chromosome Location	chr2:72620015-72620016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10084347	1.00[ASW][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[YRI][hapmap]
rs10176180	1.00[AMR][1000 genomes]
rs10188321	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10188854	1.00[AMR][1000 genomes]
rs10191381	0.92[YRI][hapmap]
rs10205704	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10206245	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs11126366	0.93[YRI][hapmap]
rs13393356	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13394873	0.85[YRI][hapmap]
rs13397743	1.00[MEX][hapmap]
rs13415635	0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs28860196	0.83[AFR][1000 genomes]
rs590345	0.85[YRI][hapmap]
rs6715775	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs6729155	0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs6749568	0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs7564660	1.00[ASW][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1005487	chr2:72464784-72819704	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv999179	chr2:72561463-72761103	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1008335	chr2:72561463-72819704	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3429281	chr2:72590346-72623676	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv874264	chr2:72593243-72901170	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv2773	chr2:72603908-72649311	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13397728	DSC3	trans	lymphoblastoid	seeQTL
rs13397728	PRRX1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72613600-72620200	Weak transcription	Fetal Brain Male	brain
2	chr2:72613800-72654000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:72619400-72620200	ZNF genes & repeats	A549	lung
4	chr2:72619600-72625400	Weak transcription	Aorta	Aorta
5	chr2:72619600-72640600	Weak transcription	Ovary	ovary
6	chr2:72620000-72620600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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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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