Variant report

Variant	rs6049694
Chromosome Location	chr20:24426523-24426524
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYNDIG1-5	chr20:24426027-24426950	NONHSAT079109

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1012631	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1012632	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13039397	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1326300	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143505	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143506	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2206643	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2206644	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223648	0.88[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2386952	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4141725	0.82[ASN][1000 genomes]
rs6036773	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036774	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036775	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036776	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036777	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036778	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036779	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036780	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036785	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6036786	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6036787	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6036788	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6036789	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6036790	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6036791	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6036792	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036793	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036796	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036798	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6036800	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6036801	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6036802	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6036803	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6049668	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6049669	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6049670	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6049671	0.81[EUR][1000 genomes]
rs6049672	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6049673	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6049675	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6049676	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6049677	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6049679	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6049680	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6049681	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6049683	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6049686	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6049687	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6049689	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049690	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049692	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049696	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6049697	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6049698	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6049699	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6049700	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6049701	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6106878	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6106881	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114716	0.80[EUR][1000 genomes]
rs6114720	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6114723	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6138295	0.81[EUR][1000 genomes]
rs6138296	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs722834	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926609	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24422800-24426600	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr20:24422800-24426600	Enhancers	H1 Cell Line	embryonic stem cell
3	chr20:24422800-24426600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr20:24422800-24426800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr20:24423000-24426600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr20:24423000-24427400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr20:24423200-24426800	Enhancers	H9 Cell Line	embryonic stem cell
8	chr20:24423400-24427600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr20:24423600-24426600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr20:24423600-24427000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr20:24424600-24426600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr20:24424800-24426600	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr20:24424800-24426600	Enhancers	Fetal Lung	lung
14	chr20:24424800-24426800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr20:24425000-24426600	Enhancers	Fetal Kidney	kidney
16	chr20:24425400-24432200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr20:24425600-24426600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr20:24425800-24429800	Enhancers	Fetal Thymus	thymus
19	chr20:24426000-24426800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
20	chr20:24426200-24427200	Enhancers	Brain Angular Gyrus	brain
21	chr20:24426200-24427200	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr20:24426400-24426600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
23	chr20:24426400-24426800	Enhancers	Brain Substantia Nigra	brain
24	chr20:24426400-24427400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr20:24426400-24427400	Enhancers	Brain Anterior Caudate	brain
26	chr20:24426400-24427400	Enhancers	Brain Hippocampus Middle	brain
27	chr20:24426400-24427600	Enhancers	Brain Cingulate Gyrus	brain
28	chr20:24426400-24427800	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links