Variant report

Variant	rs208270
Chromosome Location	chr20:41490572-41490573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs172302	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs172303	0.87[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs184075	0.94[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs208180	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs208181	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs208182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs208183	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs208184	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs208185	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs208186	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs208187	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs208188	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs208189	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs208191	0.89[CHB][hapmap];0.85[EUR][1000 genomes]
rs208192	0.82[EUR][1000 genomes]
rs208193	0.80[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.85[EUR][1000 genomes]
rs208194	0.87[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.82[EUR][1000 genomes]
rs208195	0.87[CEU][hapmap];0.85[CHB][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs208197	0.93[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs208198	0.93[CEU][hapmap];0.95[CHB][hapmap];0.87[EUR][1000 genomes]
rs208199	0.93[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs208200	0.87[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs208201	0.92[EUR][1000 genomes]
rs208269	0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs208272	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs208273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs208274	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs208275	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs208276	0.94[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4315585	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4643600	0.93[EUR][1000 genomes];0.87[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	nsv1058990	chr20:41289969-41543912	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv544277	chr20:41289969-41543912	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1063450	chr20:41409901-41880620	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1060690	chr20:41413369-41851935	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1066088	chr20:41417205-42060036	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs208270	PTPRT	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41483800-41491000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr20:41487200-41501600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr20:41490400-41494600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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