Variant report

Variant	rs1566387
Chromosome Location	chr1:224803787-224803788
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10799588	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10799589	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10916653	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564263	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.81[EUR][1000 genomes]
rs1353837	0.80[EUR][1000 genomes]
rs1499292	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566386	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566388	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1932991	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2405315	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2405317	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4654057	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654058	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs4654060	0.92[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658957	0.82[EUR][1000 genomes]
rs6665204	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690184	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs6697510	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516323	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529774	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7532595	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs883115	0.85[CEU][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes]
rs904505	0.86[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs969026	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1566387	C1orf58	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224802800-224803800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:224803000-224803800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:224803000-224803800	Flanking Active TSS	Dnd41	blood
4	chr1:224803000-224803800	Flanking Active TSS	NH-A	brain
5	chr1:224803000-224804000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
6	chr1:224803000-224804000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:224803200-224803800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
8	chr1:224803200-224803800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:224803200-224804200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
10	chr1:224803200-224804400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
11	chr1:224803200-224804400	Active TSS	NHLF	lung
12	chr1:224803200-224804600	Bivalent Enhancer	Fetal Lung	lung
13	chr1:224803200-224805800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr1:224803200-224805800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:224803200-224806400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:224803200-224806400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
17	chr1:224803200-224807000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr1:224803200-224807000	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr1:224803200-224807200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:224803200-224807400	Active TSS	NHDF-Ad	bronchial
21	chr1:224803400-224803800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:224803400-224803800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:224803400-224803800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
24	chr1:224803400-224803800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:224803400-224803800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
26	chr1:224803400-224803800	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:224803400-224803800	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:224803400-224803800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:224803400-224803800	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
30	chr1:224803400-224803800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
31	chr1:224803400-224803800	Bivalent Enhancer	Esophagus	oesophagus
32	chr1:224803400-224803800	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
33	chr1:224803400-224803800	Bivalent Enhancer	Fetal Heart	heart
34	chr1:224803400-224803800	Flanking Bivalent TSS/Enh	Ovary	ovary
35	chr1:224803400-224803800	Flanking Active TSS	Pancreas	Pancrea
36	chr1:224803400-224803800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
37	chr1:224803400-224803800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
38	chr1:224803400-224803800	Flanking Active TSS	HMEC	breast
39	chr1:224803400-224804000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
40	chr1:224803400-224804000	Bivalent Enhancer	Placenta	Placenta
41	chr1:224803400-224804000	Bivalent Enhancer	Left Ventricle	heart
42	chr1:224803400-224804000	Bivalent Enhancer	Lung	lung
43	chr1:224803400-224804000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
44	chr1:224803400-224804000	Bivalent/Poised TSS	Small Intestine	intestine
45	chr1:224803400-224804000	Bivalent Enhancer	Spleen	Spleen
46	chr1:224803400-224804200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
47	chr1:224803400-224804200	Flanking Bivalent TSS/Enh	Thymus	Thymus
48	chr1:224803400-224804400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
49	chr1:224803400-224804600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
50	chr1:224803400-224804600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood

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