Variant report

Variant	rs6796266
Chromosome Location	chr3:145254259-145254260
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11718374	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13315357	0.90[AFR][1000 genomes]
rs2077807	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2375830	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2375831	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs535300	0.90[AFR][1000 genomes]
rs55678344	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57260027	0.81[AMR][1000 genomes]
rs59611302	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60226255	0.83[AMR][1000 genomes]
rs60462007	0.85[ASN][1000 genomes]
rs60911705	0.88[ASN][1000 genomes]
rs61635697	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73872227	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7648828	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9756919	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv877587	chr3:144949453-145355433	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv877603	chr3:145098107-145260381	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv1839695	chr3:145225110-145324049	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1001259	chr3:145226633-145254795	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1002549	chr3:145226633-145255828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1000430	chr3:145226633-145256323	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1004346	chr3:145226633-145268800	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6796266	C3orf58	cis	parietal	SCAN
rs6796266	TSC22D2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145244400-145254600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:145254200-145255800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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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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