Variant report

Variant	rs1500005
Chromosome Location	chr3:46102620-46102621
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46035149..46036764-chr3:46100668..46103208,2	K562	blood:
2	chr3:46095387..46098200-chr3:46100479..46102760,2	K562	blood:
3	chr3:46100682..46102669-chr3:46103976..46105710,2	K562	blood:

Extended variants
information (count: 112 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1072755	0.80[CEU][hapmap]
rs11130080	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11130085	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130086	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11917890	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11929281	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12485978	0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs12495073	0.88[CEU][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12496322	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12630101	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs12635657	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12637023	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12639598	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs13059919	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13060901	0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs13073861	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13077099	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13077923	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13078053	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13098271	0.88[ASN][1000 genomes]
rs13434336	0.84[ASN][1000 genomes]
rs1392290	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1491959	0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];0.84[ASN][1000 genomes]
rs1546077	0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];0.81[ASN][1000 genomes]
rs1546078	0.81[ASN][1000 genomes]
rs1546079	1.00[LWK][hapmap];0.80[MEX][hapmap];1.00[YRI][hapmap]
rs1552489	0.80[CEU][hapmap]
rs1604069	0.85[ASN][1000 genomes]
rs17078495	0.80[ASN][1000 genomes]
rs17078577	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1909595	0.82[ASN][1000 genomes]
rs1909596	0.85[ASN][1000 genomes]
rs1976366	0.81[ASN][1000 genomes]
rs1976367	0.81[ASN][1000 genomes]
rs1994490	1.00[JPT][hapmap]
rs2036292	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2054866	0.80[CEU][hapmap]
rs2131091	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2201984	0.88[ASN][1000 genomes]
rs2220678	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2248228	0.87[CEU][hapmap]
rs2373153	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2373154	0.81[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap]
rs28808964	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34067839	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34381514	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34906043	0.88[ASN][1000 genomes]
rs35435608	0.88[ASN][1000 genomes]
rs35537559	0.80[ASN][1000 genomes]
rs35567508	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35657218	0.88[ASN][1000 genomes]
rs35688834	0.82[ASN][1000 genomes]
rs36111470	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3733100	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3774634	0.80[CEU][hapmap]
rs3774639	0.80[CEU][hapmap]
rs3796375	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs3821884	1.00[JPT][hapmap]
rs3851347	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4234452	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4314213	0.83[ASN][1000 genomes]
rs4333119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535265	0.80[CEU][hapmap]
rs4682800	0.84[JPT][hapmap]
rs4682806	0.83[ASN][1000 genomes]
rs4682809	0.81[ASN][1000 genomes]
rs4682810	0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4683157	0.80[CEU][hapmap]
rs4683168	0.88[ASN][1000 genomes]
rs4683175	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683178	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56307311	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59226168	0.80[ASN][1000 genomes]
rs60539039	0.91[ASN][1000 genomes]
rs62242796	0.80[ASN][1000 genomes]
rs67044455	0.80[ASN][1000 genomes]
rs6764042	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6778896	0.80[ASN][1000 genomes]
rs6780163	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs6784214	0.81[ASN][1000 genomes]
rs6794103	0.90[ASN][1000 genomes]
rs6794475	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6795629	0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6800484	0.84[ASN][1000 genomes]
rs6805094	0.91[ASN][1000 genomes]
rs6809381	0.85[CHB][hapmap]
rs730983	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs737452	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];0.80[ASN][1000 genomes]
rs751552	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs751553	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs7609756	0.82[ASN][1000 genomes]
rs7616464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623190	0.87[ASN][1000 genomes]
rs7623460	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7631598	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7642701	0.88[ASN][1000 genomes]
rs7643426	0.85[CHB][hapmap]
rs9311386	0.85[ASN][1000 genomes]
rs9311387	0.85[ASN][1000 genomes]
rs931704	0.80[ASN][1000 genomes]
rs936938	0.80[CEU][hapmap]
rs9637425	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9824886	0.85[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs9849015	0.88[ASN][1000 genomes]
rs9870445	0.85[ASN][1000 genomes]
rs9876587	0.85[ASN][1000 genomes]
rs9990063	0.84[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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv1805205	chr3:46032847-46111081	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1500005	UBA7	cis	parietal	SCAN
rs1500005	CCR1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46096400-46106200	Weak transcription	Lung	lung
2	chr3:46099000-46105400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:46100800-46103600	Weak transcription	Spleen	Spleen
4	chr3:46101000-46106400	Weak transcription	Primary B cells from cord blood	blood
5	chr3:46101200-46104200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:46101600-46107000	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr3:46101800-46104200	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr3:46102000-46103800	Weak transcription	Fetal Heart	heart
9	chr3:46102200-46105200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:46102400-46103600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:46102400-46103800	Weak transcription	GM12878-XiMat	blood
12	chr3:46102400-46105200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:46102600-46102800	Enhancers	Right Atrium	heart
14	chr3:46102600-46103000	Enhancers	Psoas Muscle	Psoas
15	chr3:46102600-46103000	Bivalent Enhancer	Osteobl	bone
16	chr3:46102600-46105600	Enhancers	Adipose Nuclei	Adipose

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