Variant report

Variant	rs6106689
Chromosome Location	chr20:23591463-23591464
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10485646	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2424563	0.81[ASN][1000 genomes]
rs2983639	0.89[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2983641	0.89[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3004142	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3004148	0.88[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35701829	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6036464	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6048927	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6106691	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62207039	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62208864	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62208869	0.83[EUR][1000 genomes]
rs7265919	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73312653	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8120131	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs984503	0.83[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6106689	CST3	cis	lymphoblastoid	seeQTL
rs6106689	XRN2	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23583400-23594000	Weak transcription	Right Atrium	heart
2	chr20:23587000-23595600	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr20:23587800-23594000	Weak transcription	Colon Smooth Muscle	Colon
4	chr20:23588200-23593400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr20:23588200-23594800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr20:23590000-23594000	Weak transcription	Brain Hippocampus Middle	brain
7	chr20:23590400-23595000	Weak transcription	Brain Anterior Caudate	brain
8	chr20:23590600-23592200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr20:23590600-23592600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr20:23591200-23593600	Weak transcription	Ovary	ovary
11	chr20:23591400-23591600	Enhancers	H9 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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