Variant report

Variant	rs868872
Chromosome Location	chr10:89950581-89950582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11202678	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12264266	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1475606	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735353	1.00[LWK][hapmap]
rs472364	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4933473	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs531325	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs533648	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs574006	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs600195	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs644440	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs652517	0.87[AMR][1000 genomes];0.90[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs868872	HTR7	cis	parietal	SCAN
rs868872	CLIC2	trans	lymphoblastoid	seeQTL
rs868872	PAPSS2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89946200-89955200	Weak transcription	Aorta	Aorta
2	chr10:89946400-89953600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr10:89946400-89955000	Weak transcription	Right Atrium	heart
4	chr10:89946400-89955200	Weak transcription	Placenta	Placenta
5	chr10:89946400-89955200	Weak transcription	Psoas Muscle	Psoas
6	chr10:89946800-89954000	Weak transcription	NHDF-Ad	bronchial
7	chr10:89949200-89952800	Weak transcription	Primary B cells from cord blood	blood
8	chr10:89949800-89951000	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr10:89949800-89951600	Enhancers	Fetal Muscle Leg	muscle
10	chr10:89949800-89956200	Enhancers	Thymus	Thymus
11	chr10:89950000-89950800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr10:89950200-89950600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr10:89950200-89951000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr10:89950400-89951000	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr10:89950400-89956400	Enhancers	Fetal Thymus	thymus

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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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