Variant report

Variant	rs3798849
Chromosome Location	chr6:55620809-55620810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1998301	0.94[ASN][1000 genomes]
rs2065024	1.00[ASN][1000 genomes]
rs2145902	0.93[ASN][1000 genomes]
rs2208601	1.00[ASN][1000 genomes]
rs2208605	0.94[ASN][1000 genomes]
rs228136	0.93[CHB][hapmap];0.83[JPT][hapmap];1.00[ASN][1000 genomes]
rs228138	1.00[ASN][1000 genomes]
rs228144	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs228145	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs228147	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs228150	0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2475248	0.94[ASN][1000 genomes]
rs2475249	0.94[ASN][1000 genomes]
rs2475251	0.94[ASN][1000 genomes]
rs2498526	0.94[ASN][1000 genomes]
rs2498527	0.94[ASN][1000 genomes]
rs2498528	0.94[ASN][1000 genomes]
rs2498531	0.94[ASN][1000 genomes]
rs6901502	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6908699	1.00[ASN][1000 genomes]
rs7743943	0.95[ASN][1000 genomes]
rs7752893	1.00[ASN][1000 genomes]
rs9357877	0.94[ASN][1000 genomes]
rs9357879	1.00[ASN][1000 genomes]
rs9370455	0.94[ASN][1000 genomes]
rs9370467	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1026411	chr6:55372845-55653498	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv885907	chr6:55539010-55621377	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv885908	chr6:55539010-55625041	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885909	chr6:55539010-55674338	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1019228	chr6:55608688-55653498	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv2752670	chr6:55614978-55781605	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55608800-55622000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:55612600-55623000	Weak transcription	Fetal Heart	heart
3	chr6:55616200-55627800	Weak transcription	Fetal Brain Male	brain
4	chr6:55618200-55672400	Weak transcription	Placenta	Placenta
5	chr6:55619600-55624600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:55619800-55621200	Weak transcription	Fetal Lung	lung
7	chr6:55619800-55626000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:55620200-55623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:55620200-55623800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr6:55620800-55621400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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