Variant report

Variant	rs6049699
Chromosome Location	chr20:24429493-24429494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1012631	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1012632	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13039397	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1326300	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2143505	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2143506	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2206643	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2206644	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2223648	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2386952	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6036773	0.80[EUR][1000 genomes]
rs6036775	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6036776	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6036777	0.85[EUR][1000 genomes]
rs6036778	0.85[EUR][1000 genomes]
rs6036779	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6036780	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6036785	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6036786	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6036787	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6036788	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6036789	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6036790	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6036791	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6036792	0.86[CEU][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6036793	0.90[CEU][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6036796	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6036798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6036801	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036802	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6036803	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6049668	0.80[EUR][1000 genomes]
rs6049670	0.80[EUR][1000 genomes]
rs6049671	0.80[EUR][1000 genomes]
rs6049672	0.80[EUR][1000 genomes]
rs6049673	0.80[EUR][1000 genomes]
rs6049675	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6049676	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6049677	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6049679	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6049680	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6049681	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6049683	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6049686	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6049687	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6049689	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6049690	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6049692	0.91[CEU][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6049694	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6049696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049698	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049700	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6049701	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6106878	0.85[EUR][1000 genomes]
rs6106881	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6114720	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6114723	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6114731	0.83[AFR][1000 genomes]
rs6138295	0.80[EUR][1000 genomes]
rs6138296	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs722834	0.91[CEU][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs926609	0.90[CEU][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][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	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1058146	chr20:24210196-24531087	Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv833946	chr20:24320375-24490702	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv458954	chr20:24410195-24431225	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv585733	chr20:24410195-24431225	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24425400-24432200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr20:24425800-24429800	Enhancers	Fetal Thymus	thymus
3	chr20:24426600-24435800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr20:24427200-24432200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr20:24427400-24436600	Weak transcription	Brain Hippocampus Middle	brain
6	chr20:24427800-24429600	Enhancers	Thymus	Thymus
7	chr20:24428200-24431400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr20:24428600-24430000	Enhancers	Primary T cells from cord blood	blood
9	chr20:24429000-24433200	Weak transcription	Gastric	stomach
10	chr20:24429000-24434200	Weak transcription	Dnd41	blood
11	chr20:24429400-24430600	Weak transcription	Fetal Intestine Large	intestine
12	chr20:24429400-24430800	Weak transcription	Stomach Mucosa	stomach
13	chr20:24429400-24431200	Weak transcription	Fetal Intestine Small	intestine
14	chr20:24429400-24434400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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