Variant report

Variant	rs6138309
Chromosome Location	chr20:24487003-24487004
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1326305	0.82[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1555892	0.85[CHD][hapmap];0.93[JPT][hapmap]
rs1980824	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1980826	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386954	0.81[CEU][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6049744	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049745	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076231	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083539	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114752	0.81[ASN][1000 genomes]
rs6132738	0.93[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs6138310	0.92[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	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1058146	chr20:24210196-24531087	Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv833946	chr20:24320375-24490702	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr20:24471200-24493600	Weak transcription	Fetal Brain Female	brain
2	chr20:24475600-24495600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr20:24479000-24488400	Weak transcription	Fetal Intestine Small	intestine
4	chr20:24481600-24504200	Weak transcription	Fetal Brain Male	brain
5	chr20:24482000-24488600	Enhancers	Left Ventricle	heart
6	chr20:24483000-24487600	Weak transcription	Right Atrium	heart
7	chr20:24483800-24488600	Enhancers	Brain Anterior Caudate	brain
8	chr20:24484000-24490000	Enhancers	Fetal Heart	heart
9	chr20:24484000-24493000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr20:24484200-24487200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr20:24484600-24487800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr20:24484600-24490600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr20:24485000-24487800	Weak transcription	Fetal Intestine Large	intestine
14	chr20:24485800-24487200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr20:24485800-24487200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr20:24485800-24487800	Weak transcription	Brain Substantia Nigra	brain
17	chr20:24486200-24487200	Enhancers	Brain Cingulate Gyrus	brain
18	chr20:24486200-24488800	Enhancers	Fetal Thymus	thymus
19	chr20:24486800-24487200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr20:24486800-24488800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr20:24486800-24488800	Enhancers	Thymus	Thymus
22	chr20:24487000-24487400	Weak transcription	Brain Angular Gyrus	brain
23	chr20:24487000-24487400	Weak transcription	Brain Hippocampus Middle	brain
24	chr20:24487000-24488400	Enhancers	Right Ventricle	heart
25	chr20:24487000-24488800	Enhancers	HMEC	breast

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