Variant report

Variant	rs12497334
Chromosome Location	chr3:54655054-54655055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13084347	0.83[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1520575	0.94[MEX][hapmap];0.82[TSI][hapmap]
rs17815840	0.94[MEX][hapmap]
rs2359861	0.83[MEX][hapmap]
rs34592432	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34836904	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36021053	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs573279	0.80[MEX][hapmap]
rs71301895	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54646800-54655200	Weak transcription	Brain Angular Gyrus	brain
2	chr3:54651000-54666400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:54652800-54665000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:54654000-54667000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:54654400-54656400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:54654600-54655800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr3:54654600-54655800	Enhancers	Fetal Muscle Trunk	muscle
8	chr3:54654800-54656200	Enhancers	HMEC	breast
9	chr3:54654800-54656200	Enhancers	HSMM	muscle
10	chr3:54654800-54662400	Weak transcription	Right Atrium	heart
11	chr3:54655000-54655200	Enhancers	Fetal Muscle Leg	muscle
12	chr3:54655000-54662400	Weak transcription	Stomach Smooth Muscle	stomach

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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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