Variant report

Variant	rs4968909
Chromosome Location	chr17:66642694-66642695
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11077693	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11077698	0.82[EUR][1000 genomes]
rs11077699	0.82[EUR][1000 genomes]
rs11657717	0.82[EUR][1000 genomes]
rs11657722	0.82[EUR][1000 genomes]
rs11658862	0.82[EUR][1000 genomes]
rs12103437	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12150366	0.80[EUR][1000 genomes]
rs17673884	0.82[EUR][1000 genomes]
rs2363280	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968913	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4968914	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[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	nsv833524	chr17:66524030-66705194	Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv908693	chr17:66619054-66647840	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4968909	TEX2	cis	parietal	SCAN
rs4968909	WIPI1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66636600-66647800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:66641600-66642800	Weak transcription	Liver	Liver
3	chr17:66642000-66644200	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr17:66642400-66643200	Enhancers	Osteobl	bone
5	chr17:66642600-66642800	Enhancers	HSMM	muscle
6	chr17:66642600-66643000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr17:66642600-66643200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr17:66642600-66643200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr17:66642600-66643200	Enhancers	Muscle Satellite Cultured Cells	--

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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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