Variant report

Variant	rs6138201
Chromosome Location	chr20:24074349-24074350
allele	G/T
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: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1005527	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1012783	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1123671	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11697353	0.85[ASN][1000 genomes]
rs11699743	0.90[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12480224	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1573008	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17249809	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1884519	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2070275	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2103922	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35663453	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55921601	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6132695	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6132696	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6132700	0.80[EUR][1000 genomes]
rs6138203	0.81[EUR][1000 genomes]
rs6138207	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138210	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61657263	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7262390	0.80[EUR][1000 genomes]
rs7270353	0.81[TSI][hapmap]
rs761863	0.81[EUR][1000 genomes]
rs910776	0.81[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6138201	CST4	cis	cerebellum	SCAN
rs6138201	CST8	cis	cerebellum	SCAN
rs6138201	CST2	cis	cerebellum	SCAN
rs6138201	INSM1	cis	parietal	SCAN

Chromatin state (count:5 , 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	chr20:24073400-24075000	Weak transcription	Placenta Amnion	Placenta Amnion

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