Variant report

Variant	rs7554672
Chromosome Location	chr1:221273158-221273159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10863578	0.82[ASN][1000 genomes]
rs11118641	0.97[ASN][1000 genomes]
rs11118648	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11118652	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118653	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11118662	0.86[EUR][1000 genomes]
rs11118663	0.86[EUR][1000 genomes]
rs11118664	0.86[EUR][1000 genomes]
rs12120171	0.84[EUR][1000 genomes]
rs12121213	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12122167	0.86[EUR][1000 genomes]
rs12123182	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12124230	0.84[EUR][1000 genomes]
rs12127195	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12128432	0.83[EUR][1000 genomes]
rs12140672	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1341619	0.86[EUR][1000 genomes]
rs1539140	0.86[EUR][1000 genomes]
rs1596173	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17009346	0.97[ASN][1000 genomes]
rs17009398	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17009529	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17009536	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1935157	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2039956	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3920857	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4142348	0.83[ASN][1000 genomes]
rs4142351	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4420085	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4427411	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4625285	0.82[ASN][1000 genomes]
rs4846684	0.81[ASN][1000 genomes]
rs4846685	0.81[ASN][1000 genomes]
rs55966903	0.97[ASN][1000 genomes]
rs57489853	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58513421	0.97[ASN][1000 genomes]
rs59098418	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61819242	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670400	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6687526	0.81[ASN][1000 genomes]
rs6693821	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6698945	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67635817	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs715300	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72742507	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7354867	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511784	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7512831	0.97[ASN][1000 genomes]
rs7515181	0.86[EUR][1000 genomes]
rs7517729	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522861	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7523927	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7526270	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539794	0.84[EUR][1000 genomes]
rs7544056	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9431057	0.86[EUR][1000 genomes]
rs9431425	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9431431	0.84[EUR][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
rs7554672	LYPLAL1	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221268000-221273600	Weak transcription	Fetal Lung	lung
2	chr1:221269400-221275000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr1:221270000-221275600	Enhancers	Adipose Nuclei	Adipose
4	chr1:221270200-221274000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr1:221270200-221276400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:221270200-221276400	Enhancers	NHDF-Ad	bronchial
7	chr1:221270400-221274400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:221270800-221275600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:221270800-221276200	Enhancers	NHLF	lung
10	chr1:221271200-221275600	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr1:221271400-221273600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:221271400-221273600	Enhancers	Spleen	Spleen
13	chr1:221271400-221273800	Enhancers	Placenta	Placenta
14	chr1:221271400-221274800	Enhancers	HUVEC	blood vessel
15	chr1:221271400-221275200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:221271400-221275800	Enhancers	Hela-S3	cervix
17	chr1:221271600-221273200	Enhancers	Primary B cells from peripheral blood	blood
18	chr1:221271600-221273400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:221271600-221274000	Enhancers	Primary B cells from cord blood	blood
20	chr1:221271600-221274200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr1:221271800-221274400	Enhancers	Primary hematopoietic stem cells	blood
22	chr1:221272000-221273200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:221272000-221273400	ZNF genes & repeats	GM12878-XiMat	blood
24	chr1:221272000-221273600	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr1:221272000-221276400	Enhancers	Osteobl	bone
26	chr1:221272200-221273600	Enhancers	Lung	lung
27	chr1:221272400-221273200	Weak transcription	Left Ventricle	heart
28	chr1:221272400-221273200	Weak transcription	A549	lung
29	chr1:221272400-221273400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:221272400-221273400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:221272400-221273600	Weak transcription	HSMMtube	muscle
32	chr1:221272400-221274600	Weak transcription	NH-A	brain
33	chr1:221272400-221276000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:221272800-221273400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:221272800-221273800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:221273000-221273200	Weak transcription	HSMM	muscle
37	chr1:221273000-221273800	Enhancers	Fetal Muscle Leg	muscle

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