Variant report

Variant	rs9817066
Chromosome Location	chr3:143537964-143537965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10212608	1.00[CEU][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11710427	0.82[CEU][hapmap]
rs11917152	0.93[GIH][hapmap];0.91[MEX][hapmap];0.87[EUR][1000 genomes]
rs12637090	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011026	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs35961568	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839664	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4839667	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4839668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62268880	0.85[EUR][1000 genomes]
rs6806661	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7641634	0.92[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs7641674	0.92[EUR][1000 genomes]
rs9822444	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824504	0.87[EUR][1000 genomes]
rs9824913	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9825095	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9838643	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs9838644	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858623	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv3418674	chr3:143457005-143558357	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1001076	chr3:143513526-143547076	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv536747	chr3:143513526-143547076	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9817066	GMPR	trans	lymphoblastoid	seeQTL
rs9817066	NANS	trans	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143514200-143544200	Weak transcription	Primary T cells from cord blood	blood
2	chr3:143529600-143540600	Weak transcription	Brain Angular Gyrus	brain
3	chr3:143529600-143543800	Weak transcription	Stomach Mucosa	stomach
4	chr3:143530000-143538800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:143530600-143539800	Weak transcription	Ovary	ovary
6	chr3:143530600-143540600	Weak transcription	Placenta	Placenta
7	chr3:143530800-143540800	Weak transcription	Fetal Stomach	stomach
8	chr3:143531000-143539800	Weak transcription	Adipose Nuclei	Adipose
9	chr3:143531000-143543200	Weak transcription	NHDF-Ad	bronchial
10	chr3:143531400-143539000	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:143531800-143539400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:143531800-143543200	Weak transcription	Aorta	Aorta
13	chr3:143533600-143543200	Weak transcription	Fetal Lung	lung
14	chr3:143533800-143539400	Weak transcription	Spleen	Spleen
15	chr3:143533800-143540600	Weak transcription	Primary B cells from cord blood	blood
16	chr3:143533800-143543200	Weak transcription	Right Atrium	heart
17	chr3:143534000-143539800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr3:143534000-143540600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:143534200-143539600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:143534200-143539800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:143534200-143540000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:143534400-143539400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:143534400-143539400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:143534400-143539800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:143534400-143540600	Weak transcription	Fetal Thymus	thymus
26	chr3:143535200-143539200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr3:143535400-143538400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr3:143536000-143545200	Weak transcription	Gastric	stomach
29	chr3:143537400-143539200	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links