Variant report

Variant	rs4438684
Chromosome Location	chr3:139016767-139016768
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:139005216..139007477-chr3:139015482..139017611,2	K562	blood:
2	chr3:139015758..139018462-chr3:139108556..139110094,2	K562	blood:
3	chr3:139010032..139013156-chr3:139014475..139018273,5	K562	blood:
4	chr3:139015801..139019925-chr3:139024525..139029594,6	K562	blood:
5	chr3:138661847..138664673-chr3:139014563..139016797,2	K562	blood:
6	chr3:139015934..139019030-chr3:139020317..139024087,4	K562	blood:
7	chr3:138667185..138669200-chr3:139015942..139017731,2	K562	blood:
8	chr3:139006378..139009772-chr3:139015328..139017740,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000244578	Chromatin interaction
ENSG00000184432	Chromatin interaction
ENSG00000248932	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12632382	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs2046965	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4894342	0.83[EUR][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	nsv591856	chr3:139000844-139037832	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1005158	chr3:139001736-139073011	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4438684	RNF7	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139007800-139018000	Weak transcription	Gastric	stomach
2	chr3:139012000-139017800	Weak transcription	HSMM	muscle
3	chr3:139012600-139018000	Weak transcription	HMEC	breast
4	chr3:139013200-139017800	Weak transcription	NHLF	lung
5	chr3:139013200-139018200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:139014000-139017400	Weak transcription	Left Ventricle	heart
7	chr3:139014200-139018200	Weak transcription	Right Ventricle	heart
8	chr3:139014200-139020200	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:139014400-139018000	Weak transcription	HSMMtube	muscle
10	chr3:139014600-139017400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:139014600-139017600	Enhancers	Liver	Liver
12	chr3:139014600-139018000	Enhancers	K562	blood
13	chr3:139014600-139020000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:139014800-139020000	Weak transcription	Right Atrium	heart
15	chr3:139015200-139017000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:139015200-139021000	Enhancers	Pancreas	Pancrea
17	chr3:139015600-139018000	Weak transcription	Ovary	ovary
18	chr3:139015600-139018200	Enhancers	Hela-S3	cervix
19	chr3:139015800-139023400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:139016200-139017200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:139016200-139020200	Enhancers	Osteobl	bone
22	chr3:139016400-139018800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:139016600-139017800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:139016600-139018000	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:139016600-139018800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:139016600-139023600	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links