Variant report

Variant	rs921163
Chromosome Location	chr2:205337400-205337401
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10490267	0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1156249	0.83[EUR][1000 genomes]
rs12990859	0.90[EUR][1000 genomes]
rs13001546	0.87[EUR][1000 genomes]
rs13003798	0.95[EUR][1000 genomes]
rs13005161	0.95[EUR][1000 genomes]
rs13007075	0.95[EUR][1000 genomes]
rs13021097	0.95[EUR][1000 genomes]
rs13024043	0.80[EUR][1000 genomes]
rs1447490	0.83[EUR][1000 genomes]
rs1550909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17637778	0.95[EUR][1000 genomes]
rs34816339	0.94[EUR][1000 genomes]
rs35207649	0.90[EUR][1000 genomes]
rs60341493	0.82[ASN][1000 genomes]
rs71427750	0.96[EUR][1000 genomes]
rs71427751	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71427753	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	esv34706	chr2:205309211-205348724	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv519470	chr2:205335630-205337400	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1012465	chr2:205335630-205349444	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs921163	ALS2CR8	cis	parietal	SCAN
rs921163	HS3ST2	trans	brain	seeQTL
rs921163	SH3BP1	trans	brain	seeQTL
rs921163	PDYN	trans	brain	seeQTL
rs921163	ADAD2	trans	brain	seeQTL
rs921163	LAMB3	trans	brain	seeQTL
rs921163	PLEKHM3	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:205335000-205341000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr2:205335200-205337400	Enhancers	K562	blood
3	chr2:205335800-205341400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:205336000-205340800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:205336400-205338200	Enhancers	NHLF	lung
6	chr2:205337000-205337400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:205337000-205337800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:205337000-205338800	Enhancers	Hela-S3	cervix
9	chr2:205337200-205337400	Enhancers	NH-A	brain
10	chr2:205337200-205337400	Flanking Active TSS	Osteobl	bone
11	chr2:205337200-205338000	Enhancers	Fetal Intestine Small	intestine
12	chr2:205337200-205338400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:205337200-205338400	Enhancers	Fetal Intestine Large	intestine
14	chr2:205337200-205338400	Enhancers	HSMMtube	muscle
15	chr2:205337400-205337600	Enhancers	Osteobl	bone
16	chr2:205337400-205344000	Weak transcription	K562	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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