Variant report

Variant	rs1197282
Chromosome Location	chr3:133052473-133052474
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TOPBP1-6	chr3:133052421-133053506	NONHSAT092182

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1109858	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs1197283	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1197285	0.84[ASN][1000 genomes]
rs1197308	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs1201674	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1209643	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12489235	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12495802	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12630350	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12633430	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637523	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12639218	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1450048	0.81[CHD][hapmap]
rs1513366	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1567788	1.00[ASW][hapmap];0.94[MEX][hapmap]
rs16840105	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16840179	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1708355	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1708357	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1708367	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1708368	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1708370	0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1795097	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1795101	0.83[CEU][hapmap];0.83[AMR][1000 genomes]
rs1992994	0.92[CEU][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2060639	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2670182	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4130893	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4854576	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4854582	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4854704	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4854708	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55686499	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55719274	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56269716	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56325413	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59171035	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59885161	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6439400	0.82[CHD][hapmap]
rs938238	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877503	chr3:133035774-133104631	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133049200-133054600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:133049600-133054600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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