Variant report

Variant	rs2056598
Chromosome Location	chr3:179741274-179741275
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11713683	0.82[ASN][1000 genomes]
rs13325101	0.85[ASN][1000 genomes]
rs1522115	0.88[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs1529269	0.85[ASN][1000 genomes]
rs1851351	0.97[ASN][1000 genomes]
rs1851352	0.86[ASN][1000 genomes]
rs1851353	0.86[ASN][1000 genomes]
rs2204095	0.88[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2339932	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.97[ASN][1000 genomes]
rs4855131	0.81[YRI][hapmap]
rs57729381	0.86[ASN][1000 genomes]
rs6443685	0.83[ASN][1000 genomes]
rs6764772	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap]
rs6788776	0.85[ASN][1000 genomes]
rs6797922	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6800148	0.88[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs73883462	0.82[ASN][1000 genomes]
rs73883468	0.82[ASN][1000 genomes]
rs73883469	0.86[ASN][1000 genomes]
rs7614706	0.97[ASN][1000 genomes]
rs7615924	0.86[ASN][1000 genomes]
rs7630527	0.82[ASN][1000 genomes]
rs7640838	0.86[ASN][1000 genomes]
rs940522	0.88[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs9809603	0.86[ASN][1000 genomes]
rs9816641	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9823631	0.83[ASN][1000 genomes]
rs9826864	0.88[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9828423	0.85[ASN][1000 genomes]
rs9828621	0.87[CHD][hapmap];0.93[JPT][hapmap]
rs9856007	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9858631	0.97[ASN][1000 genomes]
rs9866193	0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9870941	0.83[ASN][1000 genomes]
rs9881655	0.82[ASN][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	nsv829807	chr3:179527567-179745153	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv829808	chr3:179574614-179754321	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv534210	chr3:179666123-179899347	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1000756	chr3:179672703-179827373	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179726000-179754200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:179729200-179741800	Weak transcription	Dnd41	blood
3	chr3:179737000-179741600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:179740800-179741400	Active TSS	Brain Substantia Nigra	brain
5	chr3:179741000-179745200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:179741000-179750200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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