Variant report

Variant	rs6783462
Chromosome Location	chr3:56022804-56022805
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1023880	0.84[EUR][1000 genomes]
rs11713317	0.81[EUR][1000 genomes]
rs12635043	0.80[EUR][1000 genomes]
rs12635074	0.81[EUR][1000 genomes]
rs1350413	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1379721	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1379722	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1585225	0.81[EUR][1000 genomes]
rs17056290	0.83[EUR][1000 genomes]
rs17288665	0.84[EUR][1000 genomes]
rs1870273	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1914865	0.94[EUR][1000 genomes]
rs2219415	0.94[EUR][1000 genomes]
rs28450246	0.93[EUR][1000 genomes]
rs2873081	0.94[EUR][1000 genomes]
rs34309011	0.84[EUR][1000 genomes]
rs3816575	0.84[EUR][1000 genomes]
rs58120479	0.80[EUR][1000 genomes]
rs6766861	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6780386	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6799706	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73084796	0.85[EUR][1000 genomes]
rs73086151	0.80[EUR][1000 genomes]
rs73086154	0.80[EUR][1000 genomes]
rs73086189	0.83[EUR][1000 genomes]
rs73086201	0.84[EUR][1000 genomes]
rs7356061	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9809605	0.94[EUR][1000 genomes]
rs9819464	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9827086	0.94[EUR][1000 genomes]
rs9851203	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9878600	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];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	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1009709	chr3:56000827-56294945	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6783462	ABHD14A	cis	cerebellum	SCAN
rs6783462	TAF6L	trans	multi-tissue	Pritchard
rs6783462	CINP	trans	multi-tissue	Pritchard
rs6783462	ERC2	cis	parietal	SCAN
rs6783462	PEA15	trans	multi-tissue	Pritchard

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56003800-56023000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:56020600-56023600	Enhancers	Ovary	ovary
3	chr3:56021400-56023000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:56021400-56023000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:56021400-56028200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:56021400-56034800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:56021600-56023000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:56021600-56023000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:56021600-56023400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:56022000-56023600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr3:56022200-56023600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr3:56022200-56023600	Enhancers	Fetal Muscle Leg	muscle
13	chr3:56022200-56023800	Enhancers	Fetal Stomach	stomach
14	chr3:56022400-56023600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:56022400-56023600	Enhancers	Fetal Heart	heart
16	chr3:56022600-56023000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:56022600-56023800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr3:56022600-56028200	Weak transcription	Fetal Kidney	kidney
19	chr3:56022800-56023600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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