Variant report

Variant	rs12349789
Chromosome Location	chr9:86007210-86007211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10117284	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125072	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11140060	0.80[ASN][1000 genomes]
rs13299648	0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28585601	0.80[ASN][1000 genomes]
rs3860901	0.80[TSI][hapmap]
rs3860905	0.91[JPT][hapmap]
rs3860906	0.80[ASN][1000 genomes]
rs3860907	0.80[ASN][1000 genomes]
rs3860909	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs3860912	0.82[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3860913	0.82[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs3860914	0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3904187	0.93[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3904189	0.83[ASN][1000 genomes]
rs4478644	0.93[ASW][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4877757	0.84[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.80[TSI][hapmap]
rs7019165	0.83[ASN][1000 genomes]
rs7037795	0.80[ASN][1000 genomes]
rs7037928	0.80[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12349789	TLE1	cis	parietal	SCAN
rs12349789	TLE4	cis	parietal	SCAN
rs12349789	NTRK2	cis	cerebellum	SCAN
rs12349789	C9orf64	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85958200-86007600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr9:85998800-86008600	Weak transcription	Pancreas	Pancrea
3	chr9:85999400-86008400	Weak transcription	Aorta	Aorta
4	chr9:86000000-86020600	Weak transcription	Fetal Brain Female	brain
5	chr9:86004600-86014200	Weak transcription	Gastric	stomach
6	chr9:86005400-86021000	Weak transcription	Right Atrium	heart
7	chr9:86006400-86007400	Enhancers	Fetal Muscle Leg	muscle
8	chr9:86006400-86007400	Enhancers	Left Ventricle	heart
9	chr9:86006600-86007400	Enhancers	Spleen	Spleen
10	chr9:86006600-86007600	Enhancers	Fetal Intestine Large	intestine
11	chr9:86006800-86008000	Enhancers	HepG2	liver
12	chr9:86007200-86007400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:86007200-86013000	Weak transcription	Fetal Muscle Trunk	muscle

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