Variant report

Variant	rs6439890
Chromosome Location	chr3:139725259-139725260
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11929650	0.83[CHD][hapmap]
rs12497182	0.83[CHD][hapmap]
rs12638188	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1426036	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1426037	0.91[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4683772	0.91[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4683773	0.80[CHD][hapmap]
rs59433491	0.98[ASN][1000 genomes]
rs7625811	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.98[ASN][1000 genomes]
rs9289594	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][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	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv998423	chr3:139526446-139947336	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv829738	chr3:139670836-139851945	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139682600-139726000	Weak transcription	HSMMtube	muscle
2	chr3:139714400-139741200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:139722200-139733400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:139723200-139725600	Enhancers	Ovary	ovary
5	chr3:139724000-139727800	Enhancers	Fetal Muscle Leg	muscle
6	chr3:139724200-139727200	Weak transcription	Pancreas	Pancrea
7	chr3:139725200-139725400	Enhancers	Fetal Brain Male	brain
8	chr3:139725200-139725400	Enhancers	Left Ventricle	heart
9	chr3:139725200-139725600	Enhancers	Psoas Muscle	Psoas
10	chr3:139725200-139725600	Enhancers	Right Ventricle	heart
11	chr3:139725200-139728000	Enhancers	Brain Inferior Temporal Lobe	brain

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links