Variant report

Variant	rs6049668
Chromosome Location	chr20:24405065-24405066
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1012631	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1012632	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13039397	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1326300	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2143505	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2143506	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2206643	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2206644	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2223648	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap]
rs2386952	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4141725	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036774	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036775	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6036776	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6036777	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6036778	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6036779	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6036780	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6036785	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036786	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036787	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036788	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036790	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6036791	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6036792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036796	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036798	0.81[EUR][1000 genomes]
rs6036801	0.81[EUR][1000 genomes]
rs6049669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6049672	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049673	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6049675	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6049676	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6049677	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6049679	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6049680	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6049681	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6049686	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6049687	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6049689	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6049690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6049692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6049694	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6049696	0.81[EUR][1000 genomes]
rs6049697	0.81[EUR][1000 genomes]
rs6049698	0.81[EUR][1000 genomes]
rs6049699	0.80[EUR][1000 genomes]
rs6106878	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6106881	0.82[ASN][1000 genomes]
rs6114716	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6114720	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6114723	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6138295	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138296	0.86[ASN][1000 genomes]
rs722834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs926609	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24401200-24412400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr20:24403200-24405200	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr20:24403400-24411400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr20:24404000-24405200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr20:24404000-24405200	Enhancers	Brain Germinal Matrix	brain
6	chr20:24404000-24406000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr20:24404200-24405200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr20:24404200-24406800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr20:24404200-24407200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr20:24404400-24405200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr20:24404800-24405800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr20:24404800-24405800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr20:24404800-24406200	Weak transcription	Fetal Brain Male	brain
14	chr20:24404800-24406800	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links