Variant report

Variant	rs10006546
Chromosome Location	chr4:87740731-87740732
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10009590	1.00[AFR][1000 genomes]
rs10009789	0.84[MKK][hapmap]
rs10013114	0.83[MKK][hapmap]
rs10013483	0.89[AFR][1000 genomes]
rs10032048	1.00[AFR][1000 genomes]
rs10034609	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10516783	0.84[MKK][hapmap]
rs12171459	0.84[MKK][hapmap]
rs12499471	0.84[MKK][hapmap]
rs12504551	0.84[MKK][hapmap]
rs12507034	0.84[MKK][hapmap]
rs13110760	0.84[MKK][hapmap]
rs17419929	0.89[MKK][hapmap]
rs28404766	0.89[AFR][1000 genomes]
rs28452829	1.00[AFR][1000 genomes]
rs28465411	0.89[AFR][1000 genomes]
rs28470706	0.89[AFR][1000 genomes]
rs28676725	0.84[AFR][1000 genomes]
rs28718854	0.89[AFR][1000 genomes]
rs28798516	0.89[AFR][1000 genomes]
rs34226837	0.97[AFR][1000 genomes]
rs72874275	1.00[AFR][1000 genomes]
rs72874281	1.00[AFR][1000 genomes]
rs9990536	0.84[MKK][hapmap]
rs9992507	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs9994616	1.00[YRI][hapmap];0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830001	chr4:87585278-87748643	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87712600-87751400	Weak transcription	Aorta	Aorta
2	chr4:87731200-87756000	Weak transcription	Pancreas	Pancrea
3	chr4:87732400-87760000	Weak transcription	Psoas Muscle	Psoas
4	chr4:87737200-87741000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr4:87737400-87741200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr4:87737400-87743600	Weak transcription	Brain Anterior Caudate	brain
7	chr4:87737400-87744200	Weak transcription	Left Ventricle	heart
8	chr4:87737600-87742200	Weak transcription	Fetal Kidney	kidney
9	chr4:87737600-87744600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:87737600-87746600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:87737600-87752600	Weak transcription	Esophagus	oesophagus
12	chr4:87737800-87741000	Enhancers	Fetal Intestine Large	intestine
13	chr4:87737800-87754800	Weak transcription	Brain Hippocampus Middle	brain
14	chr4:87738000-87741200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:87738000-87743000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:87738200-87746800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:87738200-87752000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:87738400-87743200	Weak transcription	Adipose Nuclei	Adipose
19	chr4:87738400-87744600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:87738400-87744800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:87738400-87746400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:87738600-87741000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:87738600-87743400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:87739600-87743200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:87739800-87743200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:87739800-87757600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:87740200-87755200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:87740400-87742400	Weak transcription	NHEK	skin
29	chr4:87740400-87752000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:87740600-87741000	Weak transcription	Fetal Lung	lung

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