Variant report

Variant	rs1499865
Chromosome Location	chr20:53612272-53612273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1034095	0.81[EUR][1000 genomes]
rs1499866	0.85[AFR][1000 genomes]
rs2225319	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34385889	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34395355	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36011936	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4426578	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5014254	0.82[EUR][1000 genomes]
rs58823255	0.85[EUR][1000 genomes]
rs6014246	0.88[EUR][1000 genomes]
rs6023771	0.88[EUR][1000 genomes]
rs6023772	0.88[EUR][1000 genomes]
rs6023774	0.86[EUR][1000 genomes]
rs6092021	0.83[EUR][1000 genomes]
rs6098360	0.93[EUR][1000 genomes]
rs6098364	0.87[EUR][1000 genomes]
rs6098366	0.87[EUR][1000 genomes]
rs6098367	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6123448	0.86[EUR][1000 genomes]
rs6127362	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6127363	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6127366	0.85[EUR][1000 genomes]
rs6127367	0.87[EUR][1000 genomes]
rs928166	0.87[EUR][1000 genomes]
rs9679866	0.86[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	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
2	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv1060552	chr20:53234716-53655115	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	esv3425300	chr20:53600247-53734239	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53611600-53612800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr20:53611600-53612800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr20:53611600-53613600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr20:53611800-53612600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr20:53611800-53612600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr20:53611800-53612600	Enhancers	NH-A	brain
7	chr20:53611800-53612800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr20:53611800-53612800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr20:53611800-53612800	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr20:53612000-53612800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr20:53612200-53612400	Flanking Active TSS	Brain Germinal Matrix	brain
12	chr20:53612200-53612800	Enhancers	H9 Cell Line	embryonic stem cell

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