Variant report

Variant	rs3823039
Chromosome Location	chr6:55689305-55689306
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10456718	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs12194491	0.90[JPT][hapmap]
rs12196302	0.90[JPT][hapmap]
rs12209573	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap]
rs1447133	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17678251	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17734678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798831	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62404966	0.91[EUR][1000 genomes]
rs62404968	0.90[EUR][1000 genomes]
rs6927700	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs7769728	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs7775292	0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs921126	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs9689069	0.81[EUR][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:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55684000-55692000	Weak transcription	Fetal Brain Male	brain
2	chr6:55687200-55692400	Weak transcription	HepG2	liver
3	chr6:55687400-55690600	Enhancers	HSMMtube	muscle
4	chr6:55687600-55690000	Enhancers	Fetal Heart	heart
5	chr6:55687800-55690600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr6:55687800-55693200	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr6:55687800-55693200	Enhancers	HMEC	breast
8	chr6:55687800-55693800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:55688000-55689800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:55688000-55690200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:55688000-55690200	Weak transcription	NHLF	lung
12	chr6:55688000-55690400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:55688200-55689600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:55688200-55689600	Weak transcription	NHDF-Ad	bronchial
15	chr6:55688200-55693400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:55688600-55689600	Weak transcription	HSMM	muscle
17	chr6:55688600-55690200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:55688600-55690600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:55688800-55692000	Enhancers	Fetal Intestine Small	intestine
20	chr6:55689000-55690800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:55689000-55691000	Enhancers	Fetal Lung	lung
22	chr6:55689200-55690800	Enhancers	Colon Smooth Muscle	Colon
23	chr6:55689200-55691200	Enhancers	A549	lung
24	chr6:55689200-55693200	Enhancers	NHEK	skin
25	chr6:55689200-55693400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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