Variant report

Variant	rs2925160
Chromosome Location	chr5:114647578-114647579
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2605182	1.00[CHB][hapmap]
rs28658403	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2909844	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2909845	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925184	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2925186	1.00[JPT][hapmap]
rs2925193	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2963771	0.83[GIH][hapmap]
rs2964542	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72813857	0.80[EUR][1000 genomes]
rs9326956	1.00[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2925160	PGGT1B	cis	multi-tissue	Pritchard
rs2925160	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs2925160	SNORA13	cis	parietal	SCAN

Chromatin state (count:6 , 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	chr5:114645600-114648000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:114646400-114647600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:114646400-114648200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr5:114647400-114647800	Enhancers	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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