Variant report

Variant	rs3924916
Chromosome Location	chr13:94422191-94422192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:94422038..94423634-chr13:94425606..94427255,2	K562	blood:

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4275728	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs4366594	0.81[CEU][hapmap]
rs9584154	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948714	chr13:94100104-94699435	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv933807	chr13:94187158-94845505	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1045230	chr13:94277683-94764671	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv916694	chr13:94360053-94423063	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	nsv832684	chr13:94379507-94550853	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1130	chr13:94410849-94455628	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3924916	GPC6	cis	Artery Aorta	GTEx
rs3924916	DCT	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94415800-94423600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr13:94416600-94429000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr13:94419600-94422800	Weak transcription	Aorta	Aorta
4	chr13:94419800-94423800	Enhancers	Fetal Stomach	stomach
5	chr13:94420000-94423200	Enhancers	Fetal Intestine Large	intestine
6	chr13:94420400-94423600	Enhancers	Colon Smooth Muscle	Colon
7	chr13:94420600-94422200	Enhancers	Liver	Liver
8	chr13:94420600-94424400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr13:94420600-94429000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr13:94420800-94423200	Enhancers	HepG2	liver
11	chr13:94420800-94423800	Enhancers	Fetal Heart	heart
12	chr13:94420800-94427600	Weak transcription	A549	lung
13	chr13:94421000-94423400	Weak transcription	Fetal Kidney	kidney
14	chr13:94421400-94422200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr13:94421400-94428000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr13:94421600-94423800	Enhancers	Ovary	ovary
17	chr13:94421800-94422200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:94421800-94423000	Enhancers	Rectal Smooth Muscle	rectum
19	chr13:94421800-94423800	Enhancers	Fetal Lung	lung
20	chr13:94421800-94424400	Enhancers	Fetal Intestine Small	intestine
21	chr13:94422000-94422200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr13:94422000-94423000	Weak transcription	Fetal Brain Female	brain
23	chr13:94422000-94423600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links