Variant report

Variant	rs58990997
Chromosome Location	chr17:17453988-17453989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17447456..17449744-chr17:17453079..17454836,2	K562	blood:
2	chr17:17444761..17447453-chr17:17453663..17455413,2	K562	blood:
3	chr17:17451529..17456162-chr17:17456259..17460340,5	K562	blood:
4	chr17:17453470..17455947-chr17:17461271..17462864,2	MCF-7	breast:
5	chr17:17398601..17400670-chr17:17453497..17457003,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RASD1-3	chr17:17452335-17454556	NONHSAT146095

No data

Variant related genes	Relation type
ENSG00000108551	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12103816	1.00[EUR][1000 genomes]
rs12103822	1.00[EUR][1000 genomes]
rs3744120	1.00[EUR][1000 genomes]
rs3760186	0.83[ASN][1000 genomes]
rs4646353	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4646360	0.90[ASN][1000 genomes]
rs4646361	0.90[ASN][1000 genomes]
rs4646362	0.90[ASN][1000 genomes]
rs4646363	0.90[ASN][1000 genomes]
rs4646364	0.90[ASN][1000 genomes]
rs4646366	0.90[ASN][1000 genomes]
rs4646373	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4646374	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4646375	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4646378	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4646382	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4646384	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4646386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56046764	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58874056	0.90[ASN][1000 genomes]
rs58992576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61692723	1.00[EUR][1000 genomes]
rs70963024	1.00[EUR][1000 genomes]
rs7210045	0.90[ASN][1000 genomes]
rs73298588	0.90[ASN][1000 genomes]
rs73298590	0.90[ASN][1000 genomes]
rs73300565	0.90[ASN][1000 genomes]
rs73978955	1.00[EUR][1000 genomes]
rs73978967	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73978971	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73978972	1.00[AMR][1000 genomes]
rs73978975	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8065788	0.90[ASN][1000 genomes]
rs8066187	0.90[ASN][1000 genomes]
rs8068641	0.86[ASN][1000 genomes]
rs8076828	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs879375	1.00[EUR][1000 genomes]
rs9900054	1.00[EUR][1000 genomes]
rs9902188	1.00[EUR][1000 genomes];0.93[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	nsv482648	chr17:17315268-17455442	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv907731	chr17:17358004-17504856	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer 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	nsv907736	chr17:17381764-17465458	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv907744	chr17:17404586-17504856	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv907746	chr17:17412032-17478917	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv907747	chr17:17412032-17504856	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
8	nsv470579	chr17:17424332-17493810	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv907750	chr17:17439458-17460180	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17418200-17478000	Weak transcription	Primary T cells from cord blood	blood
2	chr17:17424600-17460000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr17:17436800-17479200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr17:17440200-17454800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr17:17442800-17456400	Weak transcription	Small Intestine	intestine
6	chr17:17443400-17467000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr17:17444000-17454400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr17:17444000-17454400	Weak transcription	Placenta	Placenta
9	chr17:17444200-17454400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr17:17444200-17467400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:17444400-17469200	Weak transcription	Fetal Brain Female	brain
12	chr17:17444600-17460400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr17:17444600-17464600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr17:17444800-17464000	Weak transcription	Esophagus	oesophagus
15	chr17:17445200-17468400	Weak transcription	Thymus	Thymus
16	chr17:17445200-17473200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr17:17447400-17461000	Weak transcription	Pancreas	Pancrea
18	chr17:17449000-17454000	Enhancers	Fetal Heart	heart
19	chr17:17449000-17454400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr17:17449000-17459000	Weak transcription	Spleen	Spleen
21	chr17:17449000-17464800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr17:17449600-17454200	Weak transcription	Adipose Nuclei	Adipose
23	chr17:17449600-17454200	Weak transcription	Gastric	stomach
24	chr17:17449600-17454600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr17:17449600-17454600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr17:17449600-17464800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:17449600-17467000	Weak transcription	Ovary	ovary
28	chr17:17449800-17454400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr17:17450200-17454000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr17:17450600-17454600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr17:17450800-17467800	Weak transcription	Brain Germinal Matrix	brain
32	chr17:17451000-17454000	Weak transcription	Stomach Mucosa	stomach
33	chr17:17451000-17455400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr17:17451000-17468400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr17:17451200-17454200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr17:17451400-17454400	Weak transcription	Fetal Brain Male	brain
37	chr17:17451400-17461200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr17:17451600-17454000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr17:17451600-17455000	Weak transcription	Right Atrium	heart
40	chr17:17451800-17454000	Weak transcription	Fetal Intestine Small	intestine
41	chr17:17451800-17454000	Weak transcription	Fetal Stomach	stomach
42	chr17:17451800-17454400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr17:17451800-17454400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr17:17451800-17454800	Weak transcription	Lung	lung
45	chr17:17452400-17454600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr17:17453000-17455200	Enhancers	Fetal Intestine Large	intestine
47	chr17:17453200-17454000	Enhancers	Brain Angular Gyrus	brain
48	chr17:17453200-17454200	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr17:17453200-17455000	Enhancers	Brain Hippocampus Middle	brain
50	chr17:17453200-17455000	Enhancers	Brain Substantia Nigra	brain

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