Variant report

Variant	rs9890334
Chromosome Location	chr17:15559082-15559083
allele	G/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:9)

rs_ID	r²[population]
rs1563011	0.84[ASN][1000 genomes]
rs2074890	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2159084	0.84[ASN][1000 genomes]
rs3760303	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4792645	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61295879	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223879	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72819876	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72819882	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	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
3	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	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
5	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv457695	chr17:15447364-15611495	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv574462	chr17:15447364-15611495	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv907704	chr17:15542933-15567196	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	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
11	nsv520426	chr17:15554561-15647723	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15552200-15564600	Weak transcription	HepG2	liver
2	chr17:15554600-15571200	Weak transcription	Liver	Liver
3	chr17:15555000-15563200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr17:15555000-15563200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr17:15555000-15587000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:15555000-15587000	Weak transcription	Gastric	stomach
7	chr17:15555200-15559200	Weak transcription	Esophagus	oesophagus
8	chr17:15555200-15562200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr17:15555200-15562200	Weak transcription	Left Ventricle	heart
10	chr17:15555200-15562200	Weak transcription	Pancreas	Pancrea
11	chr17:15555200-15564400	Weak transcription	GM12878-XiMat	blood
12	chr17:15555200-15567000	Weak transcription	Lung	lung
13	chr17:15555200-15567200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:15555200-15587000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr17:15555400-15559400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr17:15555400-15560400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr17:15555400-15560600	Weak transcription	Primary T cells from cord blood	blood
18	chr17:15555400-15561800	Weak transcription	Fetal Brain Female	brain
19	chr17:15555400-15562200	Weak transcription	Right Atrium	heart
20	chr17:15555400-15563200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr17:15555400-15564400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr17:15555400-15564600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr17:15555400-15565200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr17:15555400-15566800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr17:15555400-15567000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr17:15555400-15568200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr17:15555400-15568200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr17:15555400-15569000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr17:15555400-15576800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr17:15555400-15585800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr17:15555400-15586600	Weak transcription	Brain Angular Gyrus	brain
32	chr17:15555400-15586600	Weak transcription	Thymus	Thymus
33	chr17:15555400-15587000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr17:15555600-15559600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr17:15555600-15560800	Weak transcription	Adipose Nuclei	Adipose
36	chr17:15555600-15561200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr17:15555600-15562400	Weak transcription	Fetal Heart	heart
38	chr17:15555600-15563000	Weak transcription	Fetal Stomach	stomach
39	chr17:15555600-15563200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr17:15555600-15564600	Weak transcription	Brain Hippocampus Middle	brain
41	chr17:15555600-15565800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr17:15555600-15566400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr17:15555600-15566400	Weak transcription	NHLF	lung
44	chr17:15555600-15567000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr17:15555600-15586800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr17:15555600-15586800	Weak transcription	NHDF-Ad	bronchial
47	chr17:15555600-15587000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr17:15555600-15587200	Weak transcription	Aorta	Aorta
49	chr17:15555800-15560200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr17:15555800-15561200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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