Variant report

Variant	rs17009536
Chromosome Location	chr1:221339474-221339475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11118641	0.81[ASN][1000 genomes]
rs11118648	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11118652	0.83[ASN][1000 genomes]
rs11118653	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11118662	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11118663	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11118664	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12120171	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12121213	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12122167	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12123182	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12124230	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12126632	0.88[ASN][1000 genomes]
rs12127195	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12128432	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12140672	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1341619	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1539140	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1596173	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17009346	0.81[ASN][1000 genomes]
rs17009398	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17009529	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1935157	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2039956	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3920857	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4142351	0.83[ASN][1000 genomes]
rs4420085	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4427411	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55966903	0.81[ASN][1000 genomes]
rs57489853	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58513421	0.81[ASN][1000 genomes]
rs59093055	0.87[EUR][1000 genomes]
rs59098418	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61819242	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6670400	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6693821	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6698945	0.83[ASN][1000 genomes]
rs67635817	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs715300	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72742507	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7354867	0.83[ASN][1000 genomes]
rs7511784	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7512831	0.81[ASN][1000 genomes]
rs7515181	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7517729	0.83[ASN][1000 genomes]
rs7522861	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523927	0.83[ASN][1000 genomes]
rs7526270	0.83[ASN][1000 genomes]
rs7539794	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7544056	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7554672	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9431057	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9431425	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9431431	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv873199	chr1:221136672-221451217	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17009536	LYPLAL1	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221329400-221342600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:221334400-221339800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:221334400-221339800	Enhancers	HUVEC	blood vessel
4	chr1:221334400-221340800	Enhancers	NHDF-Ad	bronchial
5	chr1:221334800-221339600	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr1:221336000-221339600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:221336000-221341000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:221336000-221342600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:221336600-221340800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:221336600-221341600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:221336600-221342600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:221336600-221343000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:221336800-221342600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:221337000-221342400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:221337200-221340600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:221337400-221340600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr1:221337400-221342600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr1:221337600-221339800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:221338000-221339600	Weak transcription	Fetal Lung	lung
20	chr1:221338200-221339600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
21	chr1:221338600-221339800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:221338600-221342000	Enhancers	Primary hematopoietic stem cells	blood
23	chr1:221338600-221342200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:221338800-221339600	Weak transcription	Adipose Nuclei	Adipose
25	chr1:221338800-221341200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:221338800-221341800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr1:221339000-221339600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr1:221339000-221339800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:221339200-221341600	Enhancers	GM12878-XiMat	blood
30	chr1:221339400-221339600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:221339400-221339800	Enhancers	Primary B cells from cord blood	blood
32	chr1:221339400-221339800	Enhancers	Colon Smooth Muscle	Colon

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