Variant report

Variant	rs17519972
Chromosome Location	chr1:92828505-92828506
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10159094	1.00[JPT][hapmap]
rs10875319	1.00[JPT][hapmap]
rs10875349	1.00[JPT][hapmap]
rs11164226	0.89[ASN][1000 genomes]
rs11164288	1.00[JPT][hapmap]
rs11164312	0.89[ASN][1000 genomes]
rs11577572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs11577839	0.89[ASN][1000 genomes]
rs11578012	0.89[ASN][1000 genomes]
rs11578400	0.89[ASN][1000 genomes]
rs11581176	1.00[CHB][hapmap]
rs11585255	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11586355	0.94[ASN][1000 genomes]
rs11588044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs11588153	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11589858	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11803457	1.00[JPT][hapmap]
rs11804321	1.00[CHB][hapmap]
rs12094293	0.89[ASN][1000 genomes]
rs1226183	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12401372	0.89[ASN][1000 genomes]
rs12404806	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12407622	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12727665	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12729867	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12731923	0.89[ASN][1000 genomes]
rs12735898	0.89[ASN][1000 genomes]
rs12740246	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12755781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs12757533	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1483022	1.00[JPT][hapmap]
rs1487536	1.00[JPT][hapmap]
rs1487540	1.00[JPT][hapmap]
rs1542685	1.00[JPT][hapmap]
rs1809606	0.89[ASN][1000 genomes]
rs1872007	1.00[JPT][hapmap]
rs2004814	0.89[ASN][1000 genomes]
rs2046620	1.00[JPT][hapmap]
rs2087194	1.00[JPT][hapmap]
rs2391158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs2391162	0.89[ASN][1000 genomes]
rs3103176	1.00[JPT][hapmap]
rs3103178	1.00[JPT][hapmap]
rs3103181	1.00[JPT][hapmap]
rs3131814	1.00[JPT][hapmap]
rs3131828	1.00[JPT][hapmap]
rs34090353	0.89[ASN][1000 genomes]
rs35580949	0.89[ASN][1000 genomes]
rs4658294	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4658298	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4658299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs4658300	1.00[JPT][hapmap]
rs4949888	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs4970699	0.89[ASN][1000 genomes]
rs4970713	0.89[ASN][1000 genomes]
rs504606	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs515280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs519932	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs556980	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs569593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs570368	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6603962	1.00[JPT][hapmap]
rs6604082	1.00[JPT][hapmap]
rs6604090	1.00[JPT][hapmap]
rs6662379	0.89[ASN][1000 genomes]
rs6663278	1.00[JPT][hapmap]
rs6663905	0.89[ASN][1000 genomes]
rs6668803	1.00[JPT][hapmap]
rs6702267	1.00[JPT][hapmap]
rs72720457	0.89[ASN][1000 genomes]
rs7517541	1.00[JPT][hapmap]
rs7520275	1.00[JPT][hapmap]
rs7524120	0.89[ASN][1000 genomes]
rs7543947	1.00[JPT][hapmap]
rs7550680	0.89[ASN][1000 genomes]
rs9439911	0.89[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17519972	GFI1	cis	cerebellum	SCAN
rs17519972	ZNF326	cis	cerebellum	SCAN
rs17519972	PKN2	cis	cerebellum	SCAN
rs17519972	CDH24	trans	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92765800-92850000	Weak transcription	Small Intestine	intestine
2	chr1:92789800-92830600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:92792600-92846600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:92792800-92850800	Weak transcription	Fetal Heart	heart
5	chr1:92793800-92830200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:92795200-92830400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:92795200-92846600	Weak transcription	Gastric	stomach
8	chr1:92795200-92850200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:92795200-92851400	Weak transcription	Spleen	Spleen
10	chr1:92795600-92831200	Weak transcription	NHLF	lung
11	chr1:92795800-92834800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:92797800-92830800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:92798200-92846800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:92799600-92830400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:92804400-92846400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:92804400-92853200	Weak transcription	NHEK	skin
17	chr1:92804600-92830200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:92804600-92833200	Weak transcription	NH-A	brain
19	chr1:92809000-92832800	Weak transcription	Thymus	Thymus
20	chr1:92812600-92835600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:92812800-92829600	Weak transcription	Right Ventricle	heart
22	chr1:92814600-92834200	Weak transcription	Hela-S3	cervix
23	chr1:92815000-92853200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:92815400-92834400	Weak transcription	Psoas Muscle	Psoas
25	chr1:92816000-92851400	Weak transcription	A549	lung
26	chr1:92816400-92846800	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr1:92817400-92851400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:92818000-92830400	Weak transcription	GM12878-XiMat	blood
29	chr1:92818000-92831000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:92818000-92837800	Weak transcription	Esophagus	oesophagus
31	chr1:92818000-92846200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:92818000-92846400	Weak transcription	Brain Angular Gyrus	brain
33	chr1:92818000-92851600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:92818000-92852600	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:92818200-92851600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:92818600-92828800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr1:92818600-92832400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:92818800-92853000	Weak transcription	Osteobl	bone
39	chr1:92819000-92846400	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:92819800-92837800	Weak transcription	Pancreas	Pancrea
41	chr1:92819800-92838000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:92820000-92839600	Weak transcription	K562	blood
43	chr1:92823000-92831600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr1:92823600-92834800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:92823600-92853200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:92823800-92846600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:92824000-92846600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:92824000-92846600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:92824000-92851400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:92824400-92846200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links