Variant report

Variant	rs59493539
Chromosome Location	chr6:56549340-56549341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1323321	1.00[AMR][1000 genomes]
rs4413617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4520018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57183853	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57439200	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57936670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58912662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59643604	1.00[AFR][1000 genomes]
rs59801210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60143048	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60172134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60304191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60620079	1.00[AMR][1000 genomes]
rs60975519	1.00[AMR][1000 genomes]
rs61396940	0.91[AFR][1000 genomes]
rs7753074	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv432888	chr6:56507489-56560764	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56527000-56554400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr6:56529600-56553800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:56535200-56555200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:56537000-56551800	Weak transcription	Esophagus	oesophagus
5	chr6:56537200-56553400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:56537200-56555200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:56537600-56552600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:56537600-56553600	Weak transcription	Fetal Stomach	stomach
9	chr6:56537800-56549400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:56543000-56559400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:56545600-56553400	Enhancers	Brain Hippocampus Middle	brain
12	chr6:56546200-56552400	Enhancers	Brain Substantia Nigra	brain
13	chr6:56546200-56564800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:56546800-56555400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:56547000-56549800	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr6:56547200-56552200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr6:56547200-56552400	Enhancers	Brain Angular Gyrus	brain
18	chr6:56547200-56553400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:56547200-56554000	Enhancers	Brain Cingulate Gyrus	brain
20	chr6:56547200-56557400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:56547400-56549600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr6:56547400-56549600	Enhancers	Colon Smooth Muscle	Colon
23	chr6:56547400-56552400	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr6:56547400-56552400	Enhancers	Ovary	ovary
25	chr6:56547400-56552800	Enhancers	Brain Anterior Caudate	brain
26	chr6:56547400-56561600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:56547600-56549600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:56547600-56550400	Enhancers	Fetal Lung	lung
29	chr6:56547800-56549400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:56547800-56549600	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr6:56547800-56549800	Strong transcription	GM12878-XiMat	blood
32	chr6:56547800-56551800	Weak transcription	Right Ventricle	heart
33	chr6:56548000-56549400	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr6:56548000-56549400	Enhancers	NHEK	skin
35	chr6:56548000-56549600	Enhancers	Stomach Mucosa	stomach
36	chr6:56548000-56549600	Enhancers	HMEC	breast
37	chr6:56548000-56551000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:56548200-56549400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:56548200-56549400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:56548200-56549600	Enhancers	NHLF	lung
41	chr6:56548200-56549800	Enhancers	Fetal Intestine Large	intestine
42	chr6:56548200-56550000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:56548400-56549400	Weak transcription	Aorta	Aorta
44	chr6:56548400-56549400	Enhancers	Hela-S3	cervix
45	chr6:56548400-56549600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:56548400-56549600	Enhancers	NH-A	brain
47	chr6:56548600-56549600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:56548600-56549600	Enhancers	Colonic Mucosa	Colon
49	chr6:56548600-56549600	Enhancers	Duodenum Mucosa	Duodenum
50	chr6:56548600-56550400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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