Variant report

Variant	rs6072860
Chromosome Location	chr20:41393427-41393428
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1015314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12479759	1.00[CHB][hapmap]
rs1885832	1.00[CHB][hapmap]
rs1885833	1.00[CHB][hapmap]
rs2206905	1.00[CHB][hapmap]
rs3746533	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6016859	1.00[CHB][hapmap]
rs6065531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6065532	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6065533	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6065534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6072856	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6072857	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6072858	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6072859	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6072861	1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6072862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6072864	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6072865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6072866	1.00[ASN][1000 genomes]
rs6072868	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6072869	0.82[GIH][hapmap]
rs6513812	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7261386	1.00[CHB][hapmap]
rs73907265	1.00[ASN][1000 genomes]
rs9808582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[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	nsv915994	chr20:41180550-41464507	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6072860	CD40	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41392000-41393800	Weak transcription	Right Atrium	heart
2	chr20:41392800-41393800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr20:41393000-41397400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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