Variant report

Variant	rs56178618
Chromosome Location	chr17:19859536-19859537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs57853272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58524683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59395638	1.00[AMR][1000 genomes]
rs59704385	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7215558	0.86[AFR][1000 genomes]
rs7221750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980725	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980727	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980759	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73980789	0.97[AFR][1000 genomes]
rs73980794	1.00[AFR][1000 genomes]
rs73984562	0.88[AFR][1000 genomes]
rs8064839	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8066256	0.94[AFR][1000 genomes]
rs8073950	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8082216	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19840000-19879200	Weak transcription	Fetal Brain Male	brain
2	chr17:19844800-19859600	Weak transcription	HSMMtube	muscle
3	chr17:19844800-19861000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr17:19846800-19875600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr17:19850600-19861000	Weak transcription	NH-A	brain
6	chr17:19850600-19861400	Weak transcription	Gastric	stomach
7	chr17:19850600-19861600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr17:19850600-19879200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr17:19850600-19880200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr17:19850600-19880200	Weak transcription	Aorta	Aorta
11	chr17:19851600-19859800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr17:19851600-19859800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr17:19851600-19871600	Weak transcription	Colonic Mucosa	Colon
14	chr17:19852000-19861200	Weak transcription	NHLF	lung
15	chr17:19852000-19871000	Weak transcription	Small Intestine	intestine
16	chr17:19852200-19861000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr17:19852200-19861000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr17:19852200-19861200	Weak transcription	Brain Hippocampus Middle	brain
19	chr17:19852200-19861200	Weak transcription	Brain Substantia Nigra	brain
20	chr17:19852200-19861200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr17:19852200-19861400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr17:19852200-19862200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr17:19852200-19865000	Weak transcription	Ovary	ovary
24	chr17:19852200-19866000	Weak transcription	Spleen	Spleen
25	chr17:19852200-19879400	Weak transcription	Esophagus	oesophagus
26	chr17:19852200-19879600	Weak transcription	Right Ventricle	heart
27	chr17:19852200-19880000	Weak transcription	Psoas Muscle	Psoas
28	chr17:19852400-19859600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr17:19852400-19861000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr17:19852400-19861000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr17:19852400-19861000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr17:19852400-19861000	Weak transcription	HMEC	breast
33	chr17:19852400-19861200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr17:19852800-19869800	Weak transcription	Fetal Heart	heart
35	chr17:19854400-19864000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr17:19855800-19859600	Weak transcription	Left Ventricle	heart
37	chr17:19855800-19861400	Weak transcription	Pancreas	Pancrea
38	chr17:19856200-19861000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr17:19856400-19859600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr17:19856400-19860400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
41	chr17:19856600-19861800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr17:19856800-19861200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr17:19857000-19860000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr17:19857000-19868800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr17:19857200-19861200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr17:19857200-19866400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr17:19857200-19867000	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr17:19857200-19875000	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr17:19857400-19859800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr17:19857400-19860600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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