Variant report

Variant	rs16939026
Chromosome Location	chr8:49790942-49790943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10096124	1.00[CHB][hapmap]
rs12114072	1.00[LWK][hapmap]
rs1561657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16919006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16938984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16938989	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16938994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16938996	1.00[EUR][1000 genomes]
rs16939027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72640548	1.00[EUR][1000 genomes]
rs72640550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72640551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72640555	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72640561	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72640562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72640563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72640569	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7464556	0.96[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	nsv890854	chr8:49738821-49838908	Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16939026	EFCAB1	cis	brain	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:49783400-49791200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr8:49785800-49791200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:49786400-49791200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr8:49787600-49793200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr8:49789400-49791200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:49789400-49791200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr8:49789400-49791200	Weak transcription	Fetal Brain Male	brain
8	chr8:49789800-49791000	Weak transcription	Fetal Lung	lung
9	chr8:49790200-49791800	Enhancers	Fetal Brain Female	brain
10	chr8:49790400-49791400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr8:49790400-49791600	Enhancers	H1 Cell Line	embryonic stem cell
12	chr8:49790400-49792200	Enhancers	Liver	Liver
13	chr8:49790600-49791400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr8:49790800-49791600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr8:49790800-49791800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr8:49790800-49791800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr8:49790800-49791800	Enhancers	Pancreas	Pancrea

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