Variant report

Variant	rs4877757
Chromosome Location	chr9:85989187-85989188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10117284	0.84[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.80[TSI][hapmap]
rs10125072	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10125561	0.88[EUR][1000 genomes]
rs11140060	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12349789	0.84[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.80[TSI][hapmap]
rs13299648	0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2375922	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs28585601	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3849865	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3860901	0.81[CHD][hapmap];0.88[GIH][hapmap];0.90[TSI][hapmap]
rs3860902	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs3860905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3860906	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3860907	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3860909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3860912	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3860913	0.95[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3860914	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3904187	0.82[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs3904189	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4085854	0.89[EUR][1000 genomes]
rs4297106	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4478644	0.95[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4877756	0.85[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs7019165	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7037795	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7037928	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1046491	chr9:85861492-86063992	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4877757	TLE1	cis	parietal	SCAN
rs4877757	C9orf64	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85937400-85998000	Weak transcription	Aorta	Aorta
2	chr9:85958200-86007600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr9:85977000-85990200	Weak transcription	Right Ventricle	heart
4	chr9:85977400-85994600	Weak transcription	Pancreas	Pancrea
5	chr9:85977600-85990000	Weak transcription	Spleen	Spleen
6	chr9:85981000-85997800	Weak transcription	Left Ventricle	heart
7	chr9:85982600-85998800	Weak transcription	Ovary	ovary
8	chr9:85983000-85998400	Weak transcription	Fetal Brain Male	brain
9	chr9:85986400-85989200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:85986800-85989200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:85987400-85989200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:85988400-85995600	Weak transcription	HepG2	liver

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