Variant report

Variant	rs9822575
Chromosome Location	chr3:141314819-141314820
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141307980..141309540-chr3:141314236..141316394,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1077181	0.88[CEU][hapmap];0.93[MEX][hapmap]
rs11557453	0.88[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11707656	0.89[EUR][1000 genomes]
rs11709875	0.92[CEU][hapmap];0.93[MEX][hapmap]
rs11711318	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11713714	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11714208	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11716776	0.81[EUR][1000 genomes]
rs11717144	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11717842	0.96[CEU][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs12695735	0.87[CEU][hapmap]
rs12695736	0.81[EUR][1000 genomes]
rs12695740	0.96[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12695741	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12695743	0.92[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13059128	0.80[CEU][hapmap];0.93[MEX][hapmap]
rs13067519	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13068454	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13072100	0.96[CEU][hapmap];0.85[MEX][hapmap]
rs13078872	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs13083593	0.96[CEU][hapmap];0.93[MEX][hapmap];0.81[EUR][1000 genomes]
rs13084444	0.96[CEU][hapmap];0.85[MEX][hapmap];0.84[EUR][1000 genomes]
rs13088429	0.92[CEU][hapmap]
rs13095168	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13099945	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16846258	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs1863870	0.92[CEU][hapmap];0.85[MEX][hapmap]
rs2312194	0.85[EUR][1000 genomes]
rs2312266	0.89[EUR][1000 genomes]
rs34317570	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34342794	0.85[EUR][1000 genomes]
rs3732872	1.00[JPT][hapmap]
rs3806647	0.84[EUR][1000 genomes]
rs4334619	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60720666	0.85[ASN][1000 genomes]
rs6769161	1.00[JPT][hapmap]
rs71619392	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs720663	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73869619	0.83[ASN][1000 genomes]
rs73869620	0.83[ASN][1000 genomes]
rs73869622	0.83[ASN][1000 genomes]
rs73869630	0.85[ASN][1000 genomes]
rs7615579	0.85[ASN][1000 genomes]
rs7616978	0.85[ASN][1000 genomes]
rs7617073	0.85[ASN][1000 genomes]
rs7624941	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7636914	0.85[MEX][hapmap]
rs7649666	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7651511	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9289629	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.83[ASN][1000 genomes]
rs9289634	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9808953	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9823528	0.85[EUR][1000 genomes]
rs9829588	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9830055	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9833121	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9836050	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9836818	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9837202	0.92[CEU][hapmap]
rs9838230	0.85[EUR][1000 genomes]
rs9838419	0.85[EUR][1000 genomes]
rs9840159	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9840697	0.85[EUR][1000 genomes]
rs9843866	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9849180	0.96[CEU][hapmap];0.93[MEX][hapmap];0.83[EUR][1000 genomes]
rs9850416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9865971	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9868956	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs9870749	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9873042	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9822575	ZBTB38	cis	cerebellum	SCAN
rs9822575	ATP1B3	cis	cerebellum	SCAN
rs9822575	RASA2	cis	parietal	SCAN
rs9822575	RASA2	cis	cerebellum	SCAN
rs9822575	GK5	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141254800-141319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:141255200-141320000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:141255400-141319200	Weak transcription	Aorta	Aorta
4	chr3:141265200-141336200	Weak transcription	Psoas Muscle	Psoas
5	chr3:141272600-141319200	Strong transcription	Dnd41	blood
6	chr3:141275800-141320600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:141276400-141329400	Weak transcription	Small Intestine	intestine
8	chr3:141277200-141341400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:141281800-141329400	Weak transcription	Fetal Brain Male	brain
10	chr3:141288200-141320000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:141288400-141316400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:141288600-141316400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr3:141289000-141316600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:141289200-141316400	Strong transcription	Fetal Thymus	thymus
15	chr3:141293800-141319000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:141294800-141319200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:141295000-141319200	Weak transcription	Esophagus	oesophagus
18	chr3:141295200-141320000	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr3:141295600-141319600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:141295600-141320000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:141295800-141316400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:141295800-141320800	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:141296000-141316000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:141296800-141316400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:141296800-141316600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:141297600-141316400	Strong transcription	Osteobl	bone
27	chr3:141297600-141325000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:141298000-141328400	Weak transcription	Hela-S3	cervix
29	chr3:141298600-141326800	Weak transcription	Fetal Heart	heart
30	chr3:141299800-141321000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:141300200-141328800	Weak transcription	K562	blood
32	chr3:141300400-141319200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:141300600-141319000	Weak transcription	Lung	lung
34	chr3:141300600-141319000	Weak transcription	Thymus	Thymus
35	chr3:141300600-141319200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:141300600-141319200	Weak transcription	Pancreas	Pancrea
37	chr3:141300600-141319200	Weak transcription	Spleen	Spleen
38	chr3:141300600-141324600	Weak transcription	Gastric	stomach
39	chr3:141301600-141327000	Weak transcription	Brain Angular Gyrus	brain
40	chr3:141301800-141319200	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:141301800-141321000	Weak transcription	Brain Substantia Nigra	brain
42	chr3:141302000-141326800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:141303200-141316800	Strong transcription	HUVEC	blood vessel
44	chr3:141303800-141315800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:141304600-141316400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:141304600-141317600	Strong transcription	NH-A	brain
47	chr3:141304800-141316000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:141305000-141315800	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr3:141305200-141329000	Weak transcription	NHLF	lung
50	chr3:141306200-141319400	Weak transcription	NHEK	skin

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