Variant report

Variant	rs6049387
Chromosome Location	chr20:24075174-24075175
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GGTLC1-2	chr20:24071567-24075650	XLOC_013697

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1160365	0.87[EUR][1000 genomes]
rs34016617	1.00[EUR][1000 genomes]
rs34096340	0.87[EUR][1000 genomes]
rs34097439	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34123386	0.87[EUR][1000 genomes]
rs35671594	0.87[EUR][1000 genomes]
rs35675087	1.00[EUR][1000 genomes]
rs6036634	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036639	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6036641	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6036642	0.96[ASN][1000 genomes]
rs6036643	0.96[ASN][1000 genomes]
rs6036647	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6049376	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6049384	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6049385	0.97[ASN][1000 genomes]
rs6049388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049391	0.96[ASN][1000 genomes]
rs6049395	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6106785	0.83[AFR][1000 genomes]
rs6114474	0.97[ASN][1000 genomes]
rs6132697	1.00[EUR][1000 genomes]
rs6132698	1.00[EUR][1000 genomes]
rs6132699	0.89[EUR][1000 genomes]
rs6132702	0.87[EUR][1000 genomes]
rs6138198	0.97[EUR][1000 genomes]
rs6138199	1.00[EUR][1000 genomes]
rs6138206	0.95[EUR][1000 genomes]
rs6138211	0.87[EUR][1000 genomes]
rs6138213	1.00[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs62193667	1.00[EUR][1000 genomes]
rs74173629	0.89[EUR][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	nsv1056491	chr20:23955040-24105080	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6049387	SNORA2A	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24070200-24076000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr20:24070800-24075800	Weak transcription	Fetal Kidney	kidney
3	chr20:24072200-24075200	Weak transcription	Pancreas	Pancrea
4	chr20:24072600-24075200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr20:24075000-24078400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr20:24075000-24081000	Enhancers	Placenta Amnion	Placenta Amnion

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