Variant report

Variant	rs533722
Chromosome Location	chr10:89965473-89965474
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1147648	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1943987	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs485396	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs508901	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs510559	0.82[ASN][1000 genomes]
rs535541	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs537546	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs543338	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs545874	0.97[ASN][1000 genomes]
rs551265	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs567645	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs629959	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs645516	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs647730	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831940	chr10:89811247-89989199	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv895878	chr10:89959082-90006507	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv982885	chr10:89962374-89966104	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs533722	ANKRD1	cis	cerebellum	SCAN
rs533722	LRIT2	cis	cerebellum	SCAN
rs533722	CD7	trans	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89951000-89965600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr10:89955400-89998000	Weak transcription	Aorta	Aorta
3	chr10:89960800-89965600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr10:89964400-89966200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr10:89964400-89969000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr10:89964600-89966000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr10:89965000-89966200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr10:89965200-89967800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr10:89965400-89966200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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

what's new

Quick links