Variant report

Variant	rs3864939
Chromosome Location	chr12:42470065-42470066
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10880222	0.86[AMR][1000 genomes]
rs11181281	0.81[AMR][1000 genomes]
rs11181283	0.81[EUR][1000 genomes]
rs11181317	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12231330	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17090898	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17494245	0.83[AMR][1000 genomes]
rs56085053	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61942479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315650	0.98[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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1047830	chr12:42466192-42497603	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3864939	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42463800-42474600	Weak transcription	Left Ventricle	heart
2	chr12:42464600-42484000	Weak transcription	HSMM	muscle
3	chr12:42467400-42471200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr12:42468400-42490200	Weak transcription	Spleen	Spleen
5	chr12:42469400-42491800	Weak transcription	Ovary	ovary

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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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