Variant report

Variant	rs2650776
Chromosome Location	chr19:21613397-21613398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10410762	0.82[YRI][hapmap]
rs10414834	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424079	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11666213	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666447	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666525	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666540	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11667103	0.86[EUR][1000 genomes]
rs11667361	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11667392	0.80[EUR][1000 genomes]
rs11669033	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669790	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11670815	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11670868	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11672341	0.88[EUR][1000 genomes]
rs11672583	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11879901	0.87[EUR][1000 genomes]
rs12972096	0.82[YRI][hapmap]
rs13346641	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1566475	1.00[YRI][hapmap]
rs1621154	0.86[EUR][1000 genomes]
rs1626404	0.86[EUR][1000 genomes]
rs1762578	0.86[EUR][1000 genomes]
rs17680605	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1781867	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1781872	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1967182	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2061916	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2154302	0.84[EUR][1000 genomes]
rs2358993	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2359144	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2359145	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359146	1.00[YRI][hapmap]
rs2562405	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562411	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562413	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2562456	0.95[CEU][hapmap]
rs2650755	1.00[YRI][hapmap]
rs2650793	0.95[CEU][hapmap]
rs2650805	1.00[CEU][hapmap]
rs2650844	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650846	1.00[YRI][hapmap]
rs2650848	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs279807	0.81[EUR][1000 genomes]
rs279809	0.82[EUR][1000 genomes]
rs2914632	1.00[YRI][hapmap]
rs2928212	0.85[YRI][hapmap]
rs2968027	0.85[YRI][hapmap]
rs3853837	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853838	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321312	1.00[CEU][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4327181	0.86[EUR][1000 genomes]
rs4359573	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4544364	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4638726	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4808280	1.00[YRI][hapmap]
rs4809136	0.85[YRI][hapmap]
rs55756795	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55790393	0.86[EUR][1000 genomes]
rs55875743	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55899865	0.86[EUR][1000 genomes]
rs57299552	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58412280	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60173523	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61035285	0.87[EUR][1000 genomes]
rs62107465	0.84[EUR][1000 genomes]
rs62107469	0.84[EUR][1000 genomes]
rs62107472	0.86[EUR][1000 genomes]
rs62107479	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62107531	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62107532	0.88[EUR][1000 genomes]
rs62107534	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62107536	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62107539	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62107540	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62107541	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62109225	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62109226	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62109227	0.90[AMR][1000 genomes]
rs62109228	0.90[AMR][1000 genomes]
rs62109229	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62110071	0.82[EUR][1000 genomes]
rs62110367	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62110377	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62110416	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110420	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110424	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62110426	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110427	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110428	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110429	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627522	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs6511253	1.00[CEU][hapmap]
rs7246339	0.86[EUR][1000 genomes]
rs7251135	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7254098	1.00[YRI][hapmap]
rs7258099	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7258473	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7258562	0.86[EUR][1000 genomes]
rs7260065	0.95[CEU][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs73537884	0.88[EUR][1000 genomes]
rs939300	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS 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	15 gene(s)	inside rSNPs	diseases
6	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv911421	chr19:21579718-21613397	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers 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	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2650776	ZNF493	cis	parietal	SCAN
rs2650776	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs2650776	RP11-678G14.2	cis	Whole Blood	GTEx
rs2650776	RP11-678G14.2	cis	Esophagus Muscularis	GTEx
rs2650776	ZNF493	cis	cerebellum	SCAN
rs2650776	ZNF708	cis	cerebellum	SCAN
rs2650776	ZNF43	cis	parietal	SCAN
rs2650776	ZNF708	cis	lung	GTEx
rs2650776	ZNF708	cis	Thyroid	GTEx
rs2650776	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs2650776	ZNF708	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21585000-21614000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:21607600-21630200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:21613200-21613400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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