Variant report

Variant	rs2716692
Chromosome Location	chr2:39896800-39896801
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10170462	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10177801	0.87[EUR][1000 genomes]
rs10186346	1.00[CEU][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10208929	0.87[EUR][1000 genomes]
rs11124689	0.87[EUR][1000 genomes]
rs12613210	0.85[EUR][1000 genomes]
rs12712652	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12989245	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13384364	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13405084	0.95[EUR][1000 genomes]
rs13409487	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1548870	0.87[EUR][1000 genomes]
rs1548871	0.87[EUR][1000 genomes]
rs17024145	0.83[CEU][hapmap]
rs1861244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2041736	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2058618	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2160199	0.84[CEU][hapmap]
rs2215956	0.87[EUR][1000 genomes]
rs2540200	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2540247	1.00[CEU][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2540248	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2540249	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2540250	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2540251	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2540252	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2540255	1.00[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2716682	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2716683	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2716684	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2716686	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2716687	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2716688	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2716690	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2716691	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2716693	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2716694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2716719	0.87[EUR][1000 genomes]
rs2716720	0.87[EUR][1000 genomes]
rs2716732	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2716737	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2716738	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35791480	0.85[EUR][1000 genomes]
rs4670952	0.96[EUR][1000 genomes]
rs4670954	0.88[EUR][1000 genomes]
rs6707177	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6711206	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6736442	0.87[EUR][1000 genomes]
rs6748628	0.87[EUR][1000 genomes]
rs917964	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs949812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs949813	1.00[CEU][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][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	nsv873889	chr2:39830183-39950482	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2716692	THUMPD2	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39894400-39897800	Active TSS	Fetal Brain Female	brain
2	chr2:39894400-39907000	Weak transcription	Left Ventricle	heart
3	chr2:39895600-39898200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:39895600-39899600	Enhancers	Fetal Heart	heart
5	chr2:39895800-39913200	Weak transcription	Fetal Brain Male	brain
6	chr2:39896600-39896800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:39896600-39900200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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