Variant report

Variant	rs13169467
Chromosome Location	chr5:114678364-114678365
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11741985	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749663	0.86[ASN][1000 genomes]
rs13179618	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13181560	0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1350106	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17137637	1.00[ASN][1000 genomes]
rs185566	0.92[CHB][hapmap]
rs2121099	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2416412	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs267286	0.85[CHB][hapmap]
rs267287	0.85[CHB][hapmap]
rs267288	0.85[CHB][hapmap]
rs34536681	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6878783	0.95[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6886607	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6894010	0.81[AMR][1000 genomes]
rs7734039	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13169467	CCDC112	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114673000-114678400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr5:114673000-114678400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:114673600-114679200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:114674400-114682000	Weak transcription	Fetal Intestine Large	intestine
5	chr5:114677200-114679600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:114677200-114680200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:114677200-114680400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr5:114677400-114679000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:114677400-114679800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:114677400-114680200	Enhancers	Hela-S3	cervix
11	chr5:114677600-114678400	Weak transcription	Pancreas	Pancrea
12	chr5:114677600-114679000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:114678000-114679000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:114678200-114679000	Enhancers	Duodenum Mucosa	Duodenum
15	chr5:114678200-114679400	Enhancers	Fetal Intestine Small	intestine
16	chr5:114678200-114680000	Enhancers	Stomach Mucosa	stomach

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