Variant report

Variant	rs56009515
Chromosome Location	chr17:19975776-19975777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs16960662	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16960672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55814709	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55832890	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55853482	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55854412	0.87[EUR][1000 genomes]
rs55891925	0.83[EUR][1000 genomes]
rs55939726	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56002404	0.83[EUR][1000 genomes]
rs56009494	0.87[EUR][1000 genomes]
rs56034568	0.90[EUR][1000 genomes]
rs56074205	0.83[EUR][1000 genomes]
rs56186136	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56194672	0.87[EUR][1000 genomes]
rs56208903	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56267204	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56281769	0.87[EUR][1000 genomes]
rs56301435	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56344048	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7207672	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72830109	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72830114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72830123	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72830128	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72830139	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72830141	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72830145	0.87[EUR][1000 genomes]
rs72830150	0.86[EUR][1000 genomes]
rs72830153	0.87[EUR][1000 genomes]
rs72830165	0.87[EUR][1000 genomes]
rs72830176	0.87[EUR][1000 genomes]
rs72830177	0.85[EUR][1000 genomes]
rs72830178	0.87[EUR][1000 genomes]
rs72830179	0.83[EUR][1000 genomes]
rs72830188	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
4	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
5	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
6	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv907872	chr17:19945841-19996140	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1056224	chr17:19946604-19993026	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv543258	chr17:19946604-19993026	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1066594	chr17:19947874-19986671	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv543259	chr17:19947874-19986671	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19968000-19977000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr17:19968200-19977000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr17:19969200-19976600	Weak transcription	Aorta	Aorta
4	chr17:19970200-19975800	Weak transcription	NHDF-Ad	bronchial
5	chr17:19973600-19976000	Weak transcription	Primary T cells from cord blood	blood
6	chr17:19974200-19978000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr17:19974800-19976000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr17:19975000-19976400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:19975000-19976600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr17:19975200-19975800	Genic enhancers	A549	lung
11	chr17:19975200-19976000	Enhancers	Primary hematopoietic stem cells	blood
12	chr17:19975200-19976000	Enhancers	Fetal Heart	heart
13	chr17:19975200-19976600	Enhancers	Brain Hippocampus Middle	brain
14	chr17:19975200-19976600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr17:19975200-19976600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr17:19975200-19976800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr17:19975200-19977000	Enhancers	Brain Cingulate Gyrus	brain
18	chr17:19975200-19977000	Enhancers	Ovary	ovary
19	chr17:19975200-19977600	Enhancers	K562	blood
20	chr17:19975400-19976000	Enhancers	Left Ventricle	heart
21	chr17:19975400-19976400	Enhancers	GM12878-XiMat	blood
22	chr17:19975400-19976600	Enhancers	Brain Anterior Caudate	brain
23	chr17:19975400-19976800	Enhancers	Fetal Thymus	thymus
24	chr17:19975400-19977000	Enhancers	Brain Substantia Nigra	brain
25	chr17:19975400-19978000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr17:19975400-19978800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr17:19975600-19975800	Enhancers	Lung	lung
28	chr17:19975600-19976000	Enhancers	Right Atrium	heart
29	chr17:19975600-19976000	Enhancers	Right Ventricle	heart
30	chr17:19975600-19976200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr17:19975600-19976200	Enhancers	Gastric	stomach
32	chr17:19975600-19976600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr17:19975600-19976600	Enhancers	Adipose Nuclei	Adipose
34	chr17:19975600-19976600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr17:19975600-19976800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr17:19975600-19976800	Enhancers	Fetal Muscle Leg	muscle
37	chr17:19975600-19976800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr17:19975600-19977200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr17:19975600-19977600	Enhancers	Brain Germinal Matrix	brain

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