Variant report

Variant	rs2883164
Chromosome Location	chr5:49693458-49693459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10041033	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10042504	0.91[ASN][1000 genomes]
rs10055539	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10061339	0.84[ASN][1000 genomes]
rs10068272	0.81[EUR][1000 genomes]
rs10071725	0.86[ASN][1000 genomes]
rs10076490	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10079493	0.87[ASN][1000 genomes]
rs1010676	0.89[JPT][hapmap]
rs1039797	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10471362	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10471798	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10940129	0.82[EUR][1000 genomes]
rs11959569	0.87[ASN][1000 genomes]
rs12651909	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13155292	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13157992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13159506	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13168063	0.83[ASN][1000 genomes]
rs13173678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13174293	0.83[ASN][1000 genomes]
rs13180767	0.85[ASN][1000 genomes]
rs13180852	0.85[ASN][1000 genomes]
rs13182357	0.81[JPT][hapmap]
rs13185587	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13357429	0.92[ASN][1000 genomes]
rs1511735	0.81[EUR][1000 genomes]
rs1606226	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16879094	0.90[ASN][1000 genomes]
rs1811742	0.87[ASN][1000 genomes]
rs1812936	0.81[JPT][hapmap]
rs1812994	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1833900	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1849200	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1995795	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2036901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2036902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2089605	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2137132	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2137134	0.89[ASN][1000 genomes]
rs2271236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2353436	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2668024	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28445612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28500170	0.90[ASN][1000 genomes]
rs28528780	0.90[ASN][1000 genomes]
rs28661824	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28676351	0.88[ASN][1000 genomes]
rs303219	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs303231	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs303235	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs303237	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34044048	0.87[ASN][1000 genomes]
rs34044167	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34741488	0.88[ASN][1000 genomes]
rs34749302	0.88[ASN][1000 genomes]
rs34945845	0.89[ASN][1000 genomes]
rs36138717	0.89[ASN][1000 genomes]
rs3849669	0.87[ASN][1000 genomes]
rs3849670	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3860732	0.88[ASN][1000 genomes]
rs3950451	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4029989	0.85[ASN][1000 genomes]
rs4030569	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4030570	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4030571	0.88[ASN][1000 genomes]
rs4030572	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4030573	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4031137	0.87[ASN][1000 genomes]
rs4082836	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4145844	0.81[ASN][1000 genomes]
rs4340921	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4398636	0.91[ASN][1000 genomes]
rs4495185	0.92[ASN][1000 genomes]
rs4549528	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4571473	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4637546	0.85[ASN][1000 genomes]
rs4865522	0.81[EUR][1000 genomes]
rs57137858	0.90[ASN][1000 genomes]
rs57583601	0.91[ASN][1000 genomes]
rs58756661	0.90[ASN][1000 genomes]
rs59254474	0.88[ASN][1000 genomes]
rs62365887	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62365896	0.93[ASN][1000 genomes]
rs62365901	0.92[ASN][1000 genomes]
rs62365902	0.89[ASN][1000 genomes]
rs62386175	0.84[ASN][1000 genomes]
rs6450056	0.84[ASN][1000 genomes]
rs6450063	0.88[ASN][1000 genomes]
rs6450098	0.92[ASN][1000 genomes]
rs6450099	0.90[ASN][1000 genomes]
rs6450107	0.91[ASN][1000 genomes]
rs6450139	0.85[ASN][1000 genomes]
rs6868677	0.87[ASN][1000 genomes]
rs6869871	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6874829	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7446360	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7712749	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7712849	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7717982	0.90[ASN][1000 genomes]
rs7721808	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7732000	0.86[ASN][1000 genomes]
rs9292005	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019539	chr5:49455624-49702736	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv1023402	chr5:49455624-49708458	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1032003	chr5:49455624-49881491	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1023981	chr5:49584188-49871537	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv537757	chr5:49584188-49871537	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv916441	chr5:49584313-49831223	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2883164	PARP8	Cis_1M	lymphoblastoid	RTeQTL
rs2883164	LOC647121	Cis_1M	lymphoblastoid	RTeQTL
rs2883164	EMB	cis	Thyroid	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49672600-49693800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr5:49675400-49694000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr5:49676200-49693800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:49676600-49694200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr5:49681600-49694000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr5:49681800-49697200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:49682000-49719000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:49683600-49697000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:49684000-49694200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:49685000-49694200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:49685000-49695800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:49685000-49700800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:49685800-49693800	Weak transcription	Primary T cells from cord blood	blood
14	chr5:49688800-49693800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:49688800-49707200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:49688800-49710000	Weak transcription	Fetal Thymus	thymus
17	chr5:49689400-49701400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr5:49689800-49693800	Weak transcription	Fetal Intestine Large	intestine
19	chr5:49690000-49701000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr5:49690000-49701400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr5:49690200-49723600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr5:49690400-49697800	Weak transcription	Osteobl	bone
23	chr5:49690400-49708600	Strong transcription	Dnd41	blood
24	chr5:49690600-49694000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr5:49690600-49706800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:49690800-49696200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:49690800-49702600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr5:49691000-49696600	Weak transcription	HSMM	muscle
29	chr5:49691000-49702400	Weak transcription	NHEK	skin
30	chr5:49691000-49702600	Weak transcription	HMEC	breast
31	chr5:49691400-49694000	Strong transcription	Primary B cells from peripheral blood	blood
32	chr5:49691600-49693800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr5:49692000-49693800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:49692400-49698200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:49692600-49693800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr5:49692800-49695000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr5:49692800-49708000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr5:49693000-49707600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr5:49693400-49696400	Weak transcription	Primary B cells from cord blood	blood
40	chr5:49693400-49707000	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links