Variant report

Variant	rs6049455
Chromosome Location	chr20:24140927-24140928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYNDIG1-6	chr20:24139985-24141327	NONHSAT079102

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs127801	0.92[CEU][hapmap];0.95[CHB][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1496400	0.84[CEU][hapmap]
rs1587200	0.84[CEU][hapmap]
rs1884520	0.84[ASN][1000 genomes]
rs1884521	0.94[ASN][1000 genomes]
rs2013711	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2208013	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224151	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs224153	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs224154	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2749424	0.84[AMR][1000 genomes]
rs2890401	0.91[ASN][1000 genomes]
rs576373	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6036665	0.91[ASN][1000 genomes]
rs6036668	0.92[ASN][1000 genomes]
rs6036670	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6049429	0.91[ASN][1000 genomes]
rs6049432	0.88[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs6049433	0.81[CEU][hapmap]
rs6049434	0.91[ASN][1000 genomes]
rs6049435	0.91[ASN][1000 genomes]
rs6049439	0.91[ASN][1000 genomes]
rs6049443	0.91[ASN][1000 genomes]
rs6049446	0.92[ASN][1000 genomes]
rs6049453	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6049454	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6049458	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049460	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6049461	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6049467	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6083394	0.91[ASN][1000 genomes]
rs6083397	0.91[ASN][1000 genomes]
rs6114503	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6114507	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6114508	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6114509	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs761868	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs761869	0.88[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs761870	0.91[ASN][1000 genomes]
rs85687	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs85689	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs910780	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs910781	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][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	esv3328348	chr20:24095746-24285830	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6049455	CST9	cis	parietal	SCAN
rs6049455	GGTLC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24134400-24146800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:24140800-24141200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr20:24140800-24141600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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