Variant report

Variant	rs6559727
Chromosome Location	chr9:86071224-86071225
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10120060	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10746709	0.91[ASW][hapmap];0.86[CEU][hapmap];0.92[MEX][hapmap]
rs10868023	0.86[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap]
rs12343646	0.80[AMR][1000 genomes]
rs3860929	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4097648	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs4520248	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4877256	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4877772	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4877779	0.80[AMR][1000 genomes]
rs6559726	0.91[EUR][1000 genomes]
rs7019435	0.83[EUR][1000 genomes]
rs7032223	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7043389	0.86[CEU][hapmap];0.86[CHB][hapmap]
rs7043959	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs7855304	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6559727	TLE1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86056000-86085200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr9:86059600-86081000	Weak transcription	Fetal Brain Male	brain
3	chr9:86061200-86081400	Weak transcription	HepG2	liver
4	chr9:86065800-86073200	Weak transcription	Spleen	Spleen
5	chr9:86065800-86078800	Weak transcription	Left Ventricle	heart
6	chr9:86066600-86074200	Weak transcription	Pancreas	Pancrea
7	chr9:86066800-86071400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:86071000-86071400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr9:86071200-86071400	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr9:86071200-86072600	Enhancers	Rectal Mucosa Donor 29	rectum

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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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