Variant report

Variant	rs12470798
Chromosome Location	chr2:11281101-11281102
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11676692	0.83[ASN][1000 genomes]
rs11892387	0.81[AMR][1000 genomes]
rs12987119	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12987956	0.82[ASW][hapmap];1.00[YRI][hapmap]
rs13002429	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs13021587	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13027444	0.81[AMR][1000 genomes]
rs17366322	0.85[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1828930	0.92[CEU][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36026430	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55975936	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs727803	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7581322	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7586305	1.00[ASN][1000 genomes]
rs7606827	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[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	nsv520789	chr2:11259067-11312224	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12470798	PQLC3	cis	Esophagus Mucosa	GTEx
rs12470798	PQLC3	cis	Thyroid	GTEx
rs12470798	C2orf50	cis	parietal	SCAN
rs12470798	PQLC3	cis	lung	GTEx
rs12470798	IAH1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11273600-11294400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr2:11274000-11294600	Weak transcription	Right Atrium	heart
3	chr2:11280600-11281200	Enhancers	NHDF-Ad	bronchial
4	chr2:11280800-11281200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:11280800-11281200	Enhancers	Osteobl	bone

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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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