Variant report

Variant	rs569453
Chromosome Location	chr18:13076940-13076941
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10221326	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10221384	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11080620	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11663049	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12605638	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12954256	0.83[EUR][1000 genomes]
rs12955780	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1474043	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1786263	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1786270	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1786279	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1787000	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1787003	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1787004	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1787008	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1973779	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28619103	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28641764	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2902856	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35790309	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs472702	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs472992	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs473580	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs474337	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475139	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs478006	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs478399	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs482360	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs482577	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs490853	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs491349	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs492723	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs498685	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4995995	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs518145	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs527839	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529620	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs547084	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs554719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs554854	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs556371	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs556536	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs557846	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs562151	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs565832	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs567031	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs576963	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs578208	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6505775	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6505776	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6505777	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6505780	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs692833	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs692964	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71353243	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7226616	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7229870	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7233600	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7233814	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7234094	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7234960	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7236162	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7236764	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7237236	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7243660	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8088313	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8089123	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8097038	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8097125	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9783859	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9783903	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9948139	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9948681	0.81[ASN][1000 genomes]
rs9949589	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9952698	0.85[EUR][1000 genomes]
rs9958369	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9961669	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9964466	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs569453	CEP192	cis	Esophagus Muscularis	GTEx
rs569453	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs569453	CEP192	cis	Whole Blood	GTEx
rs569453	CEP192	cis	Thyroid	GTEx
rs569453	CEP192	cis	Artery Tibial	GTEx
rs569453	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs569453	CEP192	cis	Adipose Subcutaneous	GTEx
rs569453	CEP192	cis	Nerve Tibial	GTEx
rs569453	CEP192	cis	lung	GTEx
rs569453	CEP192	cis	Stomach	GTEx
rs569453	CEP192	cis	Esophagus Mucosa	GTEx
rs569453	CEP192	cis	Artery Aorta	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13018600-13117400	Weak transcription	Stomach Mucosa	stomach
2	chr18:13043200-13077800	Strong transcription	Dnd41	blood
3	chr18:13046000-13078600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr18:13048200-13095600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr18:13052200-13078200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr18:13054400-13077400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr18:13056600-13083800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr18:13056600-13095600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr18:13064800-13077400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr18:13064800-13077800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr18:13064800-13078000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr18:13065200-13078400	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr18:13065400-13078200	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr18:13065600-13079200	Strong transcription	Fetal Thymus	thymus
15	chr18:13065800-13078400	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr18:13066400-13078200	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr18:13066400-13078200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr18:13066600-13077600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr18:13066600-13077800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr18:13066600-13078200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr18:13066600-13078800	Strong transcription	Thymus	Thymus
22	chr18:13066800-13077200	Strong transcription	Liver	Liver
23	chr18:13066800-13079000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr18:13067000-13077800	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr18:13067000-13078000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr18:13067000-13079000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr18:13067000-13094600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr18:13067200-13078200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr18:13067400-13078400	Strong transcription	Primary T cells from cord blood	blood
30	chr18:13067800-13077800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr18:13067800-13077800	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr18:13067800-13078200	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr18:13068000-13077600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr18:13068000-13078200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr18:13068000-13078400	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr18:13068400-13078200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr18:13068600-13077800	Strong transcription	Brain Hippocampus Middle	brain
38	chr18:13068800-13077200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr18:13069200-13092800	Weak transcription	Small Intestine	intestine
40	chr18:13071000-13077600	Weak transcription	Right Atrium	heart
41	chr18:13071000-13095600	Weak transcription	Right Ventricle	heart
42	chr18:13071400-13095600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr18:13071600-13083800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr18:13071600-13090600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr18:13072000-13095800	Weak transcription	Fetal Brain Male	brain
46	chr18:13072200-13094400	Weak transcription	Pancreas	Pancrea
47	chr18:13072400-13095600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr18:13072800-13090800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr18:13073000-13093200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr18:13073200-13090600	Weak transcription	Brain Angular Gyrus	brain

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