Variant report

Variant	rs3798834
Chromosome Location	chr6:55688299-55688300
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10948957	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12174118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16887169	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs17733982	0.85[EUR][1000 genomes]
rs3823040	0.84[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62406248	0.82[EUR][1000 genomes]
rs9296801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9349795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9349796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9367666	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9370468	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9382559	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9396156	0.90[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	nsv1032684	chr6:55680473-55766876	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55683600-55689200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr6:55684000-55692000	Weak transcription	Fetal Brain Male	brain
3	chr6:55687200-55692400	Weak transcription	HepG2	liver
4	chr6:55687400-55688600	Enhancers	HSMM	muscle
5	chr6:55687400-55690600	Enhancers	HSMMtube	muscle
6	chr6:55687600-55690000	Enhancers	Fetal Heart	heart
7	chr6:55687800-55690600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr6:55687800-55693200	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr6:55687800-55693200	Enhancers	HMEC	breast
10	chr6:55687800-55693800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:55688000-55688600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:55688000-55688600	Enhancers	Fetal Lung	lung
13	chr6:55688000-55689000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:55688000-55689800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:55688000-55690200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:55688000-55690200	Weak transcription	NHLF	lung
17	chr6:55688000-55690400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:55688200-55688600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:55688200-55689600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:55688200-55689600	Weak transcription	NHDF-Ad	bronchial
21	chr6:55688200-55693400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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