Variant report

Variant	rs10509540
Chromosome Location	chr10:90023033-90023034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12415812	1.00[JPT][hapmap]
rs12416116	0.81[EUR][1000 genomes]
rs166976	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17110523	0.85[ASN][1000 genomes]
rs2018705	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs286487	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3781196	0.80[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3781197	0.87[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs45585838	0.85[ASN][1000 genomes]
rs60888743	0.89[EUR][1000 genomes]
rs7068821	0.83[ASW][hapmap];0.91[CEU][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7094781	0.84[ASN][1000 genomes]
rs737391	0.93[ASN][1000 genomes]
rs7922058	0.80[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs9665166	0.95[ASN][1000 genomes]
rs999951	0.80[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467414	chr10:90006507-90042154	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv895879	chr10:90015725-90219298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Type 1 diabetes	19430480	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10509540	CH25H	cis	cerebellum	SCAN
rs10509540	LIPJ	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90014200-90028400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr10:90014600-90025600	Weak transcription	Osteobl	bone
3	chr10:90019800-90023600	Enhancers	GM12878-XiMat	blood
4	chr10:90021000-90025800	Weak transcription	Dnd41	blood

Quick Search:

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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