Variant report

Variant	rs478006
Chromosome Location	chr18:13054103-13054104
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:13045915..13049710-chr18:13050964..13055431,5	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10221326	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10221384	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11080620	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11663049	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12605638	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12954256	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12955780	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1474043	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1786263	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1786270	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1786279	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1787000	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1787003	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1787004	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1787008	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1973779	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28619103	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28641764	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2902856	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35790309	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs472702	0.87[EUR][1000 genomes]
rs472992	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473580	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs474337	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs475139	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs478399	0.87[EUR][1000 genomes]
rs482360	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs482577	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs490853	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs491349	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs492723	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs498685	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4995995	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs518145	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs527839	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529620	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs547084	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs554719	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs554854	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs556371	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs556536	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs557846	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs562151	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs565832	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs567031	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569453	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs576963	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs578208	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6505775	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6505776	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6505777	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6505780	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs692833	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs692964	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353243	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7226616	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7229870	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7233600	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7233814	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7234094	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7234960	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7236162	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7236764	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7237236	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7243660	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8088313	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8089123	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8097038	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8097125	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9783859	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9783903	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9948139	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9948681	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9949589	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9951698	0.81[AMR][1000 genomes]
rs9952698	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9958369	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9961669	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9964466	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs478006	CEP192	cis	Artery Aorta	GTEx
rs478006	CEP192	cis	lung	GTEx
rs478006	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs478006	CEP192	cis	Nerve Tibial	GTEx
rs478006	CEP192	cis	Esophagus Muscularis	GTEx
rs478006	CEP192	cis	Adipose Subcutaneous	GTEx
rs478006	CEP192	cis	Stomach	GTEx
rs478006	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs478006	CEP192	cis	Whole Blood	GTEx
rs478006	CEP192	cis	Esophagus Mucosa	GTEx
rs478006	CEP192	cis	multi-tissue	Pritchard
rs478006	CEP192	cis	Artery Tibial	GTEx
rs478006	CEP192	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13017200-13056000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr18:13018600-13117400	Weak transcription	Stomach Mucosa	stomach
3	chr18:13032000-13056000	Weak transcription	HSMMtube	muscle
4	chr18:13041600-13063600	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr18:13041800-13058400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr18:13041800-13064400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr18:13043200-13056000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr18:13043200-13058400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr18:13043200-13058600	Weak transcription	Fetal Heart	heart
10	chr18:13043200-13077800	Strong transcription	Dnd41	blood
11	chr18:13045400-13063800	Strong transcription	Fetal Thymus	thymus
12	chr18:13045600-13062400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr18:13045600-13063200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr18:13045800-13056000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr18:13045800-13057000	Strong transcription	A549	lung
16	chr18:13045800-13062400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr18:13045800-13063800	Strong transcription	Duodenum Mucosa	Duodenum
18	chr18:13046000-13057600	Strong transcription	Adipose Nuclei	Adipose
19	chr18:13046000-13058200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr18:13046000-13060600	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr18:13046000-13062200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr18:13046000-13062200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr18:13046000-13062200	Strong transcription	Thymus	Thymus
24	chr18:13046000-13062400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr18:13046000-13062400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr18:13046000-13062400	Strong transcription	Fetal Intestine Large	intestine
27	chr18:13046000-13062400	Strong transcription	Fetal Muscle Leg	muscle
28	chr18:13046000-13062400	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr18:13046000-13063400	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr18:13046000-13063800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr18:13046000-13063800	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr18:13046000-13078600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr18:13046800-13062400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr18:13047200-13055200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr18:13047200-13062200	Strong transcription	Liver	Liver
36	chr18:13048000-13058800	Strong transcription	Rectal Smooth Muscle	rectum
37	chr18:13048200-13056800	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr18:13048200-13057200	Strong transcription	Brain Cingulate Gyrus	brain
39	chr18:13048200-13057800	Strong transcription	Osteobl	bone
40	chr18:13048200-13095600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr18:13048400-13057200	Strong transcription	NH-A	brain
42	chr18:13048400-13058400	Strong transcription	Left Ventricle	heart
43	chr18:13048600-13060600	Strong transcription	Hela-S3	cervix
44	chr18:13048600-13062000	Strong transcription	NHDF-Ad	bronchial
45	chr18:13048600-13062200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr18:13048800-13058000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr18:13049000-13070400	Weak transcription	Psoas Muscle	Psoas
48	chr18:13049600-13059000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr18:13049600-13061600	Strong transcription	Fetal Stomach	stomach
50	chr18:13049800-13062800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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