Variant report

Variant	rs62070980
Chromosome Location	chr17:15690046-15690047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1054119	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11651162	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11651258	0.89[EUR][1000 genomes]
rs11867683	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1561956	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1971160	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34819696	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3925260	0.89[EUR][1000 genomes]
rs4791638	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4791642	0.88[EUR][1000 genomes]
rs481648	0.88[EUR][1000 genomes]
rs62070975	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62070976	0.83[ASN][1000 genomes]
rs62070977	0.81[AMR][1000 genomes]
rs62070978	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62070981	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62071028	0.88[EUR][1000 genomes]
rs62072431	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62072433	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
4	nsv1062951	chr17:15561070-15890644	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1066023	chr17:15607267-16053512	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv907705	chr17:15611495-15717546	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
8	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
9	nsv1061222	chr17:15672934-15999778	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv442411	chr17:15677001-15694785	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island	6 gene(s)	inside rSNPs	diseases
11	esv3406800	chr17:15688452-15691000	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
12	esv3342426	chr17:15688677-15690975	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62070980	CTD-3157E16.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15686600-15690600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr17:15686600-15691400	Weak transcription	Gastric	stomach
3	chr17:15689000-15690200	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr17:15689000-15690200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr17:15689000-15690200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr17:15689200-15690200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr17:15689200-15690200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr17:15689200-15690200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr17:15689200-15690200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr17:15689200-15690200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr17:15689200-15690200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr17:15689200-15690200	Active TSS	Fetal Brain Female	brain
13	chr17:15689200-15690200	Active TSS	Fetal Intestine Small	intestine
14	chr17:15689200-15690200	Active TSS	Fetal Muscle Trunk	muscle
15	chr17:15689200-15690200	Active TSS	Ovary	ovary
16	chr17:15689200-15690200	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr17:15689200-15690200	Active TSS	Right Ventricle	heart
18	chr17:15689200-15690200	Active TSS	HSMM	muscle
19	chr17:15689200-15690200	Active TSS	NH-A	brain
20	chr17:15689200-15690200	Active TSS	Osteobl	bone
21	chr17:15689200-15690400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr17:15689200-15690400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr17:15689400-15690200	Active TSS	H1 Cell Line	embryonic stem cell
24	chr17:15689400-15690200	Active TSS	H9 Cell Line	embryonic stem cell
25	chr17:15689400-15690200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr17:15689400-15690200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr17:15689400-15690200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr17:15689400-15690200	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr17:15689400-15690200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr17:15689400-15690200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr17:15689400-15690200	Active TSS	Adipose Nuclei	Adipose
32	chr17:15689400-15690200	Active TSS	Colonic Mucosa	Colon
33	chr17:15689400-15690200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr17:15689400-15690200	Active TSS	Fetal Intestine Large	intestine
35	chr17:15689400-15690200	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr17:15689400-15690200	Active TSS	Fetal Stomach	stomach
37	chr17:15689400-15690200	Active TSS	HMEC	breast
38	chr17:15689400-15690400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr17:15689400-15690400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr17:15689600-15690200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr17:15689600-15690200	Active TSS	Brain Germinal Matrix	brain
42	chr17:15689600-15690200	Active TSS	Colon Smooth Muscle	Colon
43	chr17:15689600-15690200	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr17:15689600-15690200	Active TSS	Stomach Smooth Muscle	stomach
45	chr17:15689800-15690200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr17:15689800-15690200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr17:15689800-15690200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr17:15689800-15690200	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr17:15689800-15690200	Active TSS	Placenta	Placenta
50	chr17:15689800-15690800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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