Variant report

Variant	rs2909844
Chromosome Location	chr5:114643348-114643349
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2605182	1.00[CHB][hapmap]
rs28658403	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2909845	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925160	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925184	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2925186	1.00[JPT][hapmap]
rs2925193	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2963771	0.83[GIH][hapmap]
rs2964542	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72813857	0.82[EUR][1000 genomes]
rs9326956	1.00[JPT][hapmap]

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	nsv980960	chr5:114640484-114645980	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2909844	PGGT1B	cis	lymphoblastoid	seeQTL
rs2909844	SNORA13	cis	parietal	SCAN
rs2909844	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs2909844	PGGT1B	cis	multi-tissue	Pritchard
rs2909844	POMZP3	trans	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114642200-114651200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr5:114642200-114651400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:114642400-114647400	Weak transcription	Brain Germinal Matrix	brain

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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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