Variant report

Variant	rs578208
Chromosome Location	chr18:13068132-13068133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr18:13067884-13068465	K562	blood:	n/a	n/a

Variant related genes	Relation type
CEP192	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10221326	0.92[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10221384	0.89[CEU][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs11080620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11663049	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12605638	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12954256	0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12955780	0.88[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1474043	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1786263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1786270	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1786279	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1787000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1787003	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1787004	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1787008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1973779	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28619103	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28641764	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2902856	0.94[CHD][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35790309	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3809912	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs472702	0.92[CEU][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs472992	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs473580	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475139	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs478006	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs478399	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs482360	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs482577	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs490853	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs491349	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs492723	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs498685	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4995995	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs518145	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527839	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529620	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs547084	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs554719	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs554854	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs556371	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556536	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557846	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs562151	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565832	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567031	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs569453	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs570505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs576963	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6505775	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505776	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505777	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6505780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692833	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs692964	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71353243	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7226616	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7229870	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7233600	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7233814	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7234094	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7234960	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7236162	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7236764	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7237236	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7241536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7243660	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8088313	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8089123	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8097038	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8097125	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9783859	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9783903	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9948139	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9948681	0.85[ASN][1000 genomes]
rs9949589	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9949682	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9952698	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9958369	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9961669	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9964466	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv437176	chr18:13058494-13068132	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs578208	CEP192	cis	Whole Blood	GTEx
rs578208	CEP192	cis	Esophagus Mucosa	GTEx
rs578208	CEP192	cis	Stomach	GTEx
rs578208	CEP192	cis	Adipose Subcutaneous	GTEx
rs578208	CEP192	cis	parietal	SCAN
rs578208	CEP192	cis	Temporal Cortex	GTEx
rs578208	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs578208	CEP192	cis	cerebellum	SCAN
rs578208	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs578208	CEP192	cis	lung	GTEx
rs578208	CEP192	cis	multi-tissue	Pritchard
rs578208	CEP192	cis	Esophagus Muscularis	GTEx
rs578208	CEP192	cis	Artery Tibial	GTEx
rs578208	CEP192	cis	Thyroid	GTEx
rs578208	CEP192	cis	Brain Pons	GTEx
rs578208	CEP192	cis	Artery Aorta	GTEx
rs578208	CEP192	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 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	chr18:13049000-13070400	Weak transcription	Psoas Muscle	Psoas
6	chr18:13050800-13070800	Weak transcription	Right Atrium	heart
7	chr18:13052200-13078200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr18:13054400-13077400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr18:13056600-13068600	Weak transcription	Brain Angular Gyrus	brain
10	chr18:13056600-13083800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr18:13056600-13095600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr18:13057000-13068800	Weak transcription	Brain Substantia Nigra	brain
13	chr18:13057200-13069000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr18:13057800-13068600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr18:13058800-13069000	Weak transcription	Spleen	Spleen
16	chr18:13059000-13069000	Weak transcription	Right Ventricle	heart
17	chr18:13059400-13068600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr18:13059400-13068600	Weak transcription	Pancreas	Pancrea
19	chr18:13059400-13068800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr18:13060200-13068800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr18:13060200-13068800	Weak transcription	HSMMtube	muscle
22	chr18:13061000-13069000	Weak transcription	Colon Smooth Muscle	Colon
23	chr18:13062000-13068200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr18:13062200-13068400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr18:13062200-13068600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr18:13062400-13068600	Weak transcription	Brain Hippocampus Middle	brain
27	chr18:13062400-13068600	Weak transcription	Fetal Brain Female	brain
28	chr18:13062400-13068600	Weak transcription	Gastric	stomach
29	chr18:13062400-13075800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr18:13064400-13068600	Weak transcription	Fetal Intestine Small	intestine
31	chr18:13064800-13077400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr18:13064800-13077800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr18:13064800-13078000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr18:13065200-13076000	Strong transcription	Fetal Intestine Large	intestine
35	chr18:13065200-13076200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr18:13065200-13078400	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr18:13065400-13076200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr18:13065400-13078200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr18:13065600-13076000	Strong transcription	K562	blood
40	chr18:13065600-13079200	Strong transcription	Fetal Thymus	thymus
41	chr18:13065800-13076000	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr18:13065800-13078400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr18:13066200-13070200	Strong transcription	HepG2	liver
44	chr18:13066400-13068200	Enhancers	Primary hematopoietic stem cells	blood
45	chr18:13066400-13068400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr18:13066400-13076400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr18:13066400-13076400	Strong transcription	Fetal Muscle Leg	muscle
48	chr18:13066400-13078200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr18:13066400-13078200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr18:13066600-13070400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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