Variant report

Variant	rs11577572
Chromosome Location	chr1:92742349-92742350
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 152 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs10159094	1.00[JPT][hapmap]
rs10874637	0.85[EUR][1000 genomes]
rs10875209	1.00[JPT][hapmap]
rs10875214	1.00[JPT][hapmap]
rs10875319	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10875349	1.00[JPT][hapmap]
rs11164226	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164288	1.00[JPT][hapmap]
rs11164312	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11166141	1.00[JPT][hapmap]
rs11166144	1.00[JPT][hapmap]
rs1157469	0.88[TSI][hapmap]
rs1157470	1.00[JPT][hapmap]
rs11577839	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11578012	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11578400	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11580693	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585255	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11586355	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11586989	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11588044	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11588153	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11803457	1.00[JPT][hapmap]
rs12094293	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12119246	1.00[JPT][hapmap]
rs1226183	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1226187	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12401372	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12404806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12406749	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12407622	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12411162	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724638	0.93[CEU][hapmap]
rs12727665	0.89[ASN][1000 genomes]
rs12729867	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs12731923	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12734478	0.91[CEU][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs12735898	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12740246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12749317	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12755781	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12757533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12759512	0.83[EUR][1000 genomes]
rs1384612	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1384613	0.85[EUR][1000 genomes]
rs1483022	1.00[JPT][hapmap];0.95[TSI][hapmap]
rs1487536	1.00[JPT][hapmap]
rs1487540	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1542685	1.00[JPT][hapmap]
rs17519385	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17519972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs17578686	0.85[EUR][1000 genomes]
rs1809606	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1872007	1.00[JPT][hapmap]
rs1982720	1.00[JPT][hapmap]
rs2004814	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2046620	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2069051	0.85[EUR][1000 genomes]
rs2087194	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2093879	1.00[JPT][hapmap]
rs2128645	1.00[JPT][hapmap]
rs2128646	1.00[JPT][hapmap]
rs2391114	1.00[JPT][hapmap]
rs2391158	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2391162	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2839877	1.00[JPT][hapmap]
rs2893200	1.00[JPT][hapmap];0.88[TSI][hapmap]
rs3103176	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3103178	1.00[JPT][hapmap]
rs3103181	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3122321	0.90[ASN][1000 genomes]
rs3122327	0.81[ASN][1000 genomes]
rs3131813	0.90[ASN][1000 genomes]
rs3131814	1.00[JPT][hapmap]
rs3131827	0.90[ASN][1000 genomes]
rs3131828	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs34090353	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35015161	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35580949	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3851271	1.00[JPT][hapmap];0.88[TSI][hapmap]
rs3851272	1.00[JPT][hapmap];0.88[TSI][hapmap]
rs3851273	1.00[JPT][hapmap]
rs4437922	1.00[JPT][hapmap]
rs4658128	1.00[JPT][hapmap]
rs4658290	1.00[JPT][hapmap]
rs4658294	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4658297	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658299	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658300	1.00[JPT][hapmap]
rs488849	1.00[JPT][hapmap]
rs490800	1.00[JPT][hapmap]
rs492164	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs493595	1.00[JPT][hapmap]
rs4949888	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4970699	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4970713	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs504606	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs506375	0.84[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap]
rs507452	1.00[JPT][hapmap]
rs511546	1.00[JPT][hapmap]
rs515280	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs519932	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs527412	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs529135	1.00[JPT][hapmap]
rs534547	1.00[JPT][hapmap]
rs547699	1.00[JPT][hapmap]
rs551909	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs553861	1.00[JPT][hapmap]
rs556980	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs560389	1.00[ASW][hapmap];0.87[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs563113	0.83[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs563606	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs569593	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs570368	0.84[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap]
rs573044	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs575805	0.84[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[TSI][hapmap]
rs6603962	1.00[JPT][hapmap]
rs6603973	0.84[EUR][1000 genomes]
rs6604080	1.00[JPT][hapmap]
rs6604082	1.00[JPT][hapmap];0.95[TSI][hapmap]
rs6604090	1.00[JPT][hapmap]
rs6662379	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6662920	0.82[EUR][1000 genomes]
rs6663278	1.00[JPT][hapmap]
rs6663905	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6668803	1.00[JPT][hapmap]
rs66758257	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684317	1.00[JPT][hapmap]
rs6699855	1.00[JPT][hapmap]
rs6702267	1.00[JPT][hapmap]
rs72720457	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7517541	1.00[JPT][hapmap]
rs7520275	1.00[JPT][hapmap]
rs7522081	0.82[EUR][1000 genomes]
rs7524120	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7533077	1.00[JPT][hapmap];0.87[TSI][hapmap]
rs7542358	1.00[JPT][hapmap]
rs7542373	1.00[JPT][hapmap]
rs7543947	1.00[JPT][hapmap]
rs7545076	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs7550680	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9439911	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs981583	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv871508	chr1:92478130-92781579	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv830592	chr1:92669282-92805629	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv870667	chr1:92697188-92813741	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11577572	MT1DP	trans	cerebellum	SCAN
rs11577572	ZNF326	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92707200-92764000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:92709000-92762800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:92710000-92745200	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:92710600-92753200	Weak transcription	Small Intestine	intestine
5	chr1:92710600-92762000	Weak transcription	Fetal Brain Male	brain
6	chr1:92710600-92763400	Weak transcription	Brain Angular Gyrus	brain
7	chr1:92710600-92764000	Weak transcription	Gastric	stomach
8	chr1:92711000-92763600	Weak transcription	HSMMtube	muscle
9	chr1:92711200-92742800	Weak transcription	NHLF	lung
10	chr1:92711200-92761600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:92711200-92764000	Weak transcription	Spleen	Spleen
12	chr1:92719400-92745000	Weak transcription	Esophagus	oesophagus
13	chr1:92719400-92764000	Weak transcription	Pancreas	Pancrea
14	chr1:92719600-92760800	Weak transcription	Fetal Heart	heart
15	chr1:92720000-92763800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:92720400-92748400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:92721600-92742400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:92722400-92763400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:92723000-92763800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:92724000-92760600	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:92724200-92745000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:92724200-92746200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr1:92724200-92746400	Strong transcription	Dnd41	blood
24	chr1:92724400-92746400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:92724400-92746600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:92724600-92763800	Weak transcription	Brain Substantia Nigra	brain
27	chr1:92724800-92747400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:92725800-92764000	Weak transcription	Colonic Mucosa	Colon
29	chr1:92726400-92742400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:92726800-92746400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:92727000-92763800	Weak transcription	Right Ventricle	heart
32	chr1:92727200-92745200	Weak transcription	Lung	lung
33	chr1:92727200-92759200	Weak transcription	A549	lung
34	chr1:92727200-92763800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:92729800-92763800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:92731400-92745000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:92731400-92751200	Weak transcription	GM12878-XiMat	blood
38	chr1:92732000-92750800	Weak transcription	Fetal Kidney	kidney
39	chr1:92732000-92763600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:92732600-92745000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:92732800-92742400	Weak transcription	NHDF-Ad	bronchial
42	chr1:92733000-92743600	Strong transcription	Fetal Intestine Large	intestine
43	chr1:92733000-92749200	Strong transcription	Fetal Thymus	thymus
44	chr1:92733600-92754800	Weak transcription	HMEC	breast
45	chr1:92734400-92742800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:92734800-92743800	Strong transcription	Primary B cells from cord blood	blood
47	chr1:92735000-92743000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:92735000-92743600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:92735200-92752400	Weak transcription	Psoas Muscle	Psoas
50	chr1:92735600-92742600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links