Variant report

Variant	rs13078747
Chromosome Location	chr3:53573517-53573518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12629517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34106488	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35131285	0.87[ASN][1000 genomes]
rs3774426	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs56021416	0.92[EUR][1000 genomes]
rs6777794	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6777870	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs991818	0.86[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13078747	NEK4	cis	parietal	SCAN
rs13078747	RNF123	cis	parietal	SCAN
rs13078747	NT5DC2	cis	parietal	SCAN
rs13078747	ITIH3	cis	parietal	SCAN
rs13078747	DCP1A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53560600-53587000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:53564800-53579400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:53566400-53583200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:53567800-53579400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:53569400-53574200	Weak transcription	Fetal Intestine Small	intestine
6	chr3:53569400-53581800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:53569600-53581800	Weak transcription	Fetal Intestine Large	intestine
8	chr3:53570600-53579200	Weak transcription	Fetal Lung	lung
9	chr3:53571000-53577600	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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