Variant report

Variant	rs6049796
Chromosome Location	chr20:24571454-24571455
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs16986777	1.00[CEU][hapmap]
rs16986779	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[AMR][1000 genomes]
rs4813525	0.85[JPT][hapmap]
rs4815280	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs4815281	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs4815283	0.86[JPT][hapmap]
rs6036845	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6036850	0.85[JPT][hapmap]
rs6049798	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs6049801	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6049803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6049804	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6049809	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6083557	0.84[EUR][1000 genomes]
rs6106914	0.91[AMR][1000 genomes]
rs6106915	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes]
rs6114791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6114802	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62215308	0.98[EUR][1000 genomes]
rs62215309	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62215310	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7268328	0.80[AMR][1000 genomes]
rs73098723	0.93[EUR][1000 genomes]
rs742803	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6049796	FBXO48	trans	cerebellum	SCAN
rs6049796	ACSS1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24568200-24574600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:24568200-24577400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:24568800-24573800	Weak transcription	Fetal Heart	heart
4	chr20:24568800-24575800	Weak transcription	Brain Substantia Nigra	brain
5	chr20:24569200-24573800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr20:24571400-24584800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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