Variant report

Variant	rs4494918
Chromosome Location	chr3:51683248-51683249
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11709482	0.80[AMR][1000 genomes]
rs11719995	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11917683	1.00[CEU][hapmap]
rs11919197	0.85[CEU][hapmap]
rs13090011	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3821829	0.85[CEU][hapmap]
rs4067	0.85[CEU][hapmap]
rs4234644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4317086	0.84[EUR][1000 genomes]
rs4355273	0.85[CEU][hapmap]
rs4468965	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4687721	1.00[CEU][hapmap]
rs4687770	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap]
rs4687771	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6775666	0.85[CEU][hapmap]
rs6787312	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9841077	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9864443	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9864693	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9866430	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv997264	chr3:51584056-51689648	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536570	chr3:51584056-51689648	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv999553	chr3:51584056-51696052	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4494918	HYAL2	cis	parietal	SCAN
rs4494918	IQCF2	cis	parietal	SCAN
rs4494918	MST1	cis	cerebellum	SCAN
rs4494918	TEX264	cis	Nerve Tibial	GTEx
rs4494918	HEMK1	cis	cerebellum	SCAN
rs4494918	TEX264	cis	Esophagus Muscularis	GTEx
rs4494918	TEX264	cis	Artery Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51661000-51684200	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr3:51672000-51683400	Strong transcription	Liver	Liver
3	chr3:51677600-51684200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:51680000-51696000	Weak transcription	A549	lung
5	chr3:51680400-51684200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:51680600-51683400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:51680600-51692600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:51680800-51691400	Weak transcription	GM12878-XiMat	blood
9	chr3:51680800-51702800	Weak transcription	K562	blood
10	chr3:51681000-51684200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:51681000-51688000	Weak transcription	HSMMtube	muscle
12	chr3:51681000-51689000	Weak transcription	Hela-S3	cervix
13	chr3:51681000-51689600	Weak transcription	HepG2	liver
14	chr3:51681000-51689600	Weak transcription	NH-A	brain
15	chr3:51681000-51689600	Weak transcription	NHLF	lung
16	chr3:51681000-51689800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:51681000-51693400	Weak transcription	Fetal Brain Male	brain
18	chr3:51681000-51697000	Weak transcription	Stomach Mucosa	stomach
19	chr3:51681200-51689000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:51681200-51689400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:51681200-51693800	Weak transcription	NHDF-Ad	bronchial
22	chr3:51681400-51687800	Weak transcription	Primary T cells from cord blood	blood
23	chr3:51681400-51688600	Weak transcription	HMEC	breast
24	chr3:51681400-51689400	Weak transcription	HSMM	muscle
25	chr3:51681600-51703200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:51681800-51689200	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:51682000-51691400	Weak transcription	NHEK	skin
28	chr3:51682200-51683600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:51682200-51684400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:51682200-51691400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:51682200-51691400	Weak transcription	Pancreas	Pancrea
32	chr3:51682200-51704400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:51682400-51683400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:51682400-51683400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:51682400-51683600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:51682400-51688000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:51682400-51688000	Weak transcription	Osteobl	bone
38	chr3:51682400-51688200	Weak transcription	Right Ventricle	heart
39	chr3:51682400-51688800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:51682400-51689400	Weak transcription	Spleen	Spleen
41	chr3:51682400-51689400	Weak transcription	Dnd41	blood
42	chr3:51682400-51689600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:51682400-51689600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:51682400-51689600	Weak transcription	Gastric	stomach
45	chr3:51682400-51689800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:51682400-51690000	Weak transcription	Brain Substantia Nigra	brain
47	chr3:51682400-51691600	Weak transcription	Psoas Muscle	Psoas
48	chr3:51682400-51692400	Weak transcription	Colonic Mucosa	Colon
49	chr3:51682400-51693600	Weak transcription	Fetal Kidney	kidney
50	chr3:51682400-51696200	Weak transcription	Placenta Amnion	Placenta Amnion

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