Variant report

Variant	rs4502547
Chromosome Location	chr3:139965072-139965073
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11717409	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4266155	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4371479	0.84[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4423726	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs4518083	0.94[ASN][1000 genomes]
rs4683816	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs62267960	0.81[ASN][1000 genomes]
rs6439912	0.85[CHD][hapmap]
rs6789431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73870712	1.00[ASN][1000 genomes]
rs73870714	0.87[ASN][1000 genomes]
rs73870715	0.87[ASN][1000 genomes]
rs7431715	0.84[AFR][1000 genomes]
rs967861	0.85[CHD][hapmap]
rs9811609	0.81[CEU][hapmap]
rs9840502	0.86[AFR][1000 genomes]
rs9844835	0.92[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs9846393	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9861445	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829739	chr3:139797496-140002685	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv432486	chr3:139924092-140049121	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv829740	chr3:139925767-140106169	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139958600-139967400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:139962000-139970600	Weak transcription	Ovary	ovary
3	chr3:139962600-139966400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:139963000-139965200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:139963200-139965400	Enhancers	HSMMtube	muscle
6	chr3:139963200-139969800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:139963400-139968000	Weak transcription	Right Atrium	heart
8	chr3:139963400-139968600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:139964000-139971600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:139964400-139968600	Weak transcription	Adipose Nuclei	Adipose
11	chr3:139964600-139966600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:139964800-139968600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:139964800-139970400	Weak transcription	HSMM	muscle

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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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