Variant report

Variant	rs9893179
Chromosome Location	chr17:17452512-17452513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17451529..17456162-chr17:17456259..17460340,5	K562	blood:

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

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11651620	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11654842	0.90[ASN][1000 genomes]
rs11656215	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11867345	0.86[EUR][1000 genomes]
rs11871667	0.85[EUR][1000 genomes]
rs12939945	0.86[EUR][1000 genomes]
rs12941371	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12945144	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12948060	0.89[ASN][1000 genomes]
rs1531100	0.88[EUR][1000 genomes]
rs2124344	0.83[ASN][1000 genomes]
rs4244596	0.89[ASN][1000 genomes]
rs4244598	0.89[ASN][1000 genomes]
rs4646350	0.89[ASN][1000 genomes]
rs4646351	0.89[ASN][1000 genomes]
rs4646352	0.88[EUR][1000 genomes]
rs4646356	0.88[EUR][1000 genomes]
rs4646357	0.89[ASN][1000 genomes]
rs4646358	0.88[EUR][1000 genomes]
rs4646359	0.88[EUR][1000 genomes]
rs4646365	0.88[EUR][1000 genomes]
rs4646368	0.88[EUR][1000 genomes]
rs4646370	0.89[ASN][1000 genomes]
rs4646372	0.89[ASN][1000 genomes]
rs4646385	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4646387	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4646388	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4646390	0.96[ASN][1000 genomes]
rs4646391	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4646392	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4646394	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4646395	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4646396	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6502603	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7209113	0.89[ASN][1000 genomes]
rs7221487	0.89[ASN][1000 genomes]
rs729974	0.89[ASN][1000 genomes]
rs744925	0.88[EUR][1000 genomes]
rs747770	0.96[ASN][1000 genomes]
rs750546	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8079427	0.89[ASN][1000 genomes]
rs8080165	0.95[ASN][1000 genomes]
rs8082417	0.86[ASN][1000 genomes]
rs897450	0.86[EUR][1000 genomes]
rs897451	0.89[ASN][1000 genomes]
rs936108	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9892560	0.95[ASN][1000 genomes]
rs9894321	0.95[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:60 , 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	chr17:17439800-17453200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr17:17440000-17453200	Weak transcription	Brain Substantia Nigra	brain
6	chr17:17440200-17454800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr17:17442800-17456400	Weak transcription	Small Intestine	intestine
8	chr17:17443400-17467000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr17:17444000-17454400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr17:17444000-17454400	Weak transcription	Placenta	Placenta
11	chr17:17444200-17454400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr17:17444200-17467400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:17444400-17469200	Weak transcription	Fetal Brain Female	brain
14	chr17:17444600-17460400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr17:17444600-17464600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr17:17444800-17464000	Weak transcription	Esophagus	oesophagus
17	chr17:17445200-17468400	Weak transcription	Thymus	Thymus
18	chr17:17445200-17473200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr17:17447400-17461000	Weak transcription	Pancreas	Pancrea
20	chr17:17449000-17454000	Enhancers	Fetal Heart	heart
21	chr17:17449000-17454400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr17:17449000-17459000	Weak transcription	Spleen	Spleen
23	chr17:17449000-17464800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr17:17449200-17453200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr17:17449600-17454200	Weak transcription	Adipose Nuclei	Adipose
26	chr17:17449600-17454200	Weak transcription	Gastric	stomach
27	chr17:17449600-17454600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr17:17449600-17454600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr17:17449600-17464800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr17:17449600-17467000	Weak transcription	Ovary	ovary
31	chr17:17449800-17453400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr17:17449800-17454400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr17:17450000-17453200	Weak transcription	Brain Hippocampus Middle	brain
34	chr17:17450200-17454000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr17:17450400-17453000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr17:17450600-17454600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr17:17450800-17453800	Weak transcription	Fetal Muscle Leg	muscle
38	chr17:17450800-17467800	Weak transcription	Brain Germinal Matrix	brain
39	chr17:17451000-17453000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr17:17451000-17454000	Weak transcription	Stomach Mucosa	stomach
41	chr17:17451000-17455400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr17:17451000-17468400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr17:17451200-17454200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr17:17451400-17454400	Weak transcription	Fetal Brain Male	brain
45	chr17:17451400-17461200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr17:17451600-17453600	Weak transcription	Right Ventricle	heart
47	chr17:17451600-17454000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr17:17451600-17455000	Weak transcription	Right Atrium	heart
49	chr17:17451800-17453000	Weak transcription	Fetal Intestine Large	intestine
50	chr17:17451800-17453200	Weak transcription	Brain Angular Gyrus	brain

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