Variant report

Variant	rs13003798
Chromosome Location	chr2:205355768-205355769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10490267	1.00[CHB][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1156249	0.83[EUR][1000 genomes]
rs12990859	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13001546	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13005161	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13007075	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13010221	0.83[AMR][1000 genomes]
rs13021097	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13024043	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1447490	0.83[EUR][1000 genomes]
rs1550909	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17637637	0.83[AMR][1000 genomes]
rs17637778	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34816339	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35207649	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71427750	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71427751	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71427753	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs921163	1.00[CEU][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.95[EUR][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	nsv964353	chr2:205303005-205473935	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13003798	PLEKHM3	cis	cerebellum	SCAN
rs13003798	LAMB3	trans	brain	seeQTL
rs13003798	HS3ST2	trans	brain	seeQTL
rs13003798	ADAD2	trans	brain	seeQTL
rs13003798	PDYN	trans	brain	seeQTL
rs13003798	SH3BP1	trans	brain	seeQTL
rs13003798	ALS2CR8	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:205351800-205359800	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:205352000-205356000	Weak transcription	Osteobl	bone
3	chr2:205352800-205355800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:205352800-205356000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr2:205352800-205356000	Weak transcription	NHDF-Ad	bronchial
6	chr2:205353000-205356000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:205353000-205356200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:205353200-205356000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:205355200-205357000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:205355600-205356600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:205355600-205356800	Enhancers	NHEK	skin

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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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