Variant report

Variant	rs1044708
Chromosome Location	chr2:211298180-211298181
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10195342	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1027901	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1044710	0.85[LWK][hapmap]
rs10804181	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10804182	0.86[EUR][1000 genomes]
rs10804183	0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs11889228	0.86[EUR][1000 genomes]
rs11894867	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11896108	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11900468	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12469589	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12473150	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12477237	0.81[EUR][1000 genomes]
rs1350463	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1379838	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1812875	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2021214	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2287424	0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2287425	0.86[EUR][1000 genomes]
rs2287429	0.86[EUR][1000 genomes]
rs2287430	0.86[EUR][1000 genomes]
rs2287432	0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2287433	0.89[CEU][hapmap];0.83[CHB][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2370949	0.86[EUR][1000 genomes]
rs2370956	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2887899	0.86[EUR][1000 genomes]
rs35314871	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3755184	0.89[EUR][1000 genomes]
rs3770689	0.86[EUR][1000 genomes]
rs3770694	0.86[EUR][1000 genomes]
rs3770695	0.86[EUR][1000 genomes]
rs3770699	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3821136	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845633	0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs3851937	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3856339	0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs3863852	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4102441	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41272663	0.99[ASN][1000 genomes]
rs4467201	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4609985	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4673526	0.96[EUR][1000 genomes]
rs4673528	0.81[EUR][1000 genomes]
rs4673529	0.83[EUR][1000 genomes]
rs6435568	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6435569	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6717228	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6745925	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6756422	0.86[EUR][1000 genomes]
rs725379	0.86[EUR][1000 genomes]
rs7575005	0.99[ASN][1000 genomes]
rs7578688	0.86[EUR][1000 genomes]
rs7595022	0.86[EUR][1000 genomes]
rs7893	0.85[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012567	chr2:211087588-211315554	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv875767	chr2:211119233-211334647	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv3147	chr2:211281479-211326844	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1044708	UNC80	cis	lymphoblastoid	seeQTL
rs1044708	CRYGB	cis	cerebellum	SCAN
rs1044708	CPS1	cis	parietal	SCAN
rs1044708	LANCL1	cis	cerebellum	SCAN
rs1044708	CPS1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211287200-211298200	Weak transcription	HMEC	breast
2	chr2:211287200-211299200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:211287200-211299600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:211290600-211299000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:211291400-211299400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:211291600-211299000	Weak transcription	Lung	lung
7	chr2:211291600-211300800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:211291800-211299600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:211292400-211323000	Weak transcription	Fetal Brain Male	brain
10	chr2:211293000-211299400	Weak transcription	Esophagus	oesophagus
11	chr2:211293000-211305800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:211293200-211299000	Weak transcription	Brain Germinal Matrix	brain
13	chr2:211293200-211299000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:211293200-211299200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:211293200-211307400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr2:211293200-211307800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:211293200-211311600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:211293400-211299000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:211293600-211299000	Weak transcription	Pancreas	Pancrea
20	chr2:211293800-211298400	Weak transcription	Hela-S3	cervix
21	chr2:211293800-211299400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:211293800-211299400	Weak transcription	Spleen	Spleen
23	chr2:211293800-211335400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:211294200-211299200	Enhancers	Fetal Heart	heart
25	chr2:211294200-211301400	Strong transcription	Primary T cells from cord blood	blood
26	chr2:211294400-211303400	Weak transcription	NHLF	lung
27	chr2:211294800-211306200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:211294800-211306400	Strong transcription	Dnd41	blood
29	chr2:211294800-211322200	Weak transcription	K562	blood
30	chr2:211294800-211333200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:211295000-211306600	Strong transcription	Brain Cingulate Gyrus	brain
32	chr2:211295000-211307400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:211295000-211330400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:211295000-211336000	Weak transcription	Colonic Mucosa	Colon
35	chr2:211295000-211340600	Weak transcription	HUVEC	blood vessel
36	chr2:211295200-211299000	Weak transcription	Placenta	Placenta
37	chr2:211295200-211299400	Weak transcription	Right Ventricle	heart
38	chr2:211295400-211309200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:211295600-211301800	Strong transcription	Stomach Smooth Muscle	stomach
40	chr2:211295600-211302000	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr2:211295600-211302400	Strong transcription	Primary hematopoietic stem cells	blood
42	chr2:211295600-211302400	Strong transcription	Brain Hippocampus Middle	brain
43	chr2:211295600-211305200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:211295600-211306200	Strong transcription	Adipose Nuclei	Adipose
45	chr2:211295600-211306600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:211295600-211307800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:211295600-211308000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr2:211295800-211301600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:211295800-211302600	Strong transcription	Liver	Liver
50	chr2:211295800-211302600	Strong transcription	Fetal Brain Female	brain

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