Variant report

Variant	rs239550
Chromosome Location	chr6:80683107-80683108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1007416	0.82[CHB][hapmap]
rs12663071	0.93[ASN][1000 genomes]
rs12663092	1.00[ASN][1000 genomes]
rs13201038	0.88[CHB][hapmap]
rs1355576	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1398161	0.88[CHB][hapmap]
rs149293	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1512120	1.00[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs151586	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151650	0.83[ASN][1000 genomes]
rs151666	0.82[CHB][hapmap]
rs151674	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891260	0.88[CHB][hapmap]
rs1818439	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2117446	0.99[ASN][1000 genomes]
rs2322554	0.88[CHB][hapmap]
rs239506	0.98[ASN][1000 genomes]
rs239508	0.82[ASN][1000 genomes]
rs239520	0.88[CHB][hapmap]
rs239526	0.88[CHB][hapmap]
rs239529	0.88[CHB][hapmap]
rs239532	0.88[CHB][hapmap]
rs239545	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs239546	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239547	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs239551	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991	0.88[CHB][hapmap]
rs343623	0.88[CHB][hapmap]
rs343628	0.88[CHB][hapmap]
rs343629	0.88[CHB][hapmap]
rs343705	0.88[CHB][hapmap]
rs35626280	0.99[ASN][1000 genomes]
rs3812153	0.88[CHB][hapmap]
rs4552689	0.84[ASN][1000 genomes]
rs4706821	0.96[ASN][1000 genomes]
rs4706822	0.95[CEU][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60373337	1.00[ASN][1000 genomes]
rs6915142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6918121	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6939120	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7743696	0.88[CHB][hapmap]
rs7754628	0.88[CHB][hapmap]
rs865264	0.88[CHB][hapmap]
rs9294167	0.98[ASN][1000 genomes]
rs9343948	0.98[ASN][1000 genomes]
rs9343950	0.98[ASN][1000 genomes]
rs9343951	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9343952	0.83[ASN][1000 genomes]
rs9343956	1.00[ASN][1000 genomes]
rs9350836	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9352786	0.99[ASN][1000 genomes]
rs9352787	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9361576	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9361578	0.82[ASN][1000 genomes]
rs9448857	0.88[CHB][hapmap]
rs9448863	0.88[CHB][hapmap]

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	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv965652	chr6:80663704-80688769	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs239550	SLC25A38	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80682600-80687800	Weak transcription	Fetal Thymus	thymus

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