Variant report

Variant	rs12953783
Chromosome Location	chr18:13082782-13082783
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10163827	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11080617	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11080618	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11661559	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11662634	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11664213	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11664469	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12327306	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12605267	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12607398	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12957380	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12960349	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12961596	0.89[ASN][1000 genomes]
rs12963426	0.91[ASN][1000 genomes]
rs12967249	0.84[AMR][1000 genomes]
rs12970503	0.89[ASN][1000 genomes]
rs13381134	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13381779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17603207	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17659689	0.87[ASN][1000 genomes]
rs17659749	0.87[ASN][1000 genomes]
rs17659896	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2282540	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2282541	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28551661	0.91[ASN][1000 genomes]
rs28654613	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34117444	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34166083	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34302481	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35368962	0.88[ASN][1000 genomes]
rs35563947	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3976787	0.89[ASN][1000 genomes]
rs496270	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs68004799	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71353241	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7228684	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7229869	0.83[EUR][1000 genomes]
rs7230391	0.91[ASN][1000 genomes]
rs7234938	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7236710	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7239486	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8083401	0.82[ASN][1000 genomes]
rs8089724	0.89[ASN][1000 genomes]
rs8090667	0.87[ASN][1000 genomes]
rs8093576	0.87[ASN][1000 genomes]
rs8566	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9950241	0.89[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12953783	CEP192	cis	Artery Tibial	GTEx
rs12953783	CEP192	cis	lung	GTEx
rs12953783	CEP192	cis	Nerve Tibial	GTEx
rs12953783	CEP192	cis	Thyroid	GTEx
rs12953783	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs12953783	CEP192	cis	Esophagus Muscularis	GTEx

Chromatin state (count:121 , 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	chr18:13048200-13095600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr18:13056600-13083800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr18:13056600-13095600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr18:13067000-13094600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr18:13069200-13092800	Weak transcription	Small Intestine	intestine
7	chr18:13071000-13095600	Weak transcription	Right Ventricle	heart
8	chr18:13071400-13095600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr18:13071600-13083800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr18:13071600-13090600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr18:13072000-13095800	Weak transcription	Fetal Brain Male	brain
12	chr18:13072200-13094400	Weak transcription	Pancreas	Pancrea
13	chr18:13072400-13095600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr18:13072800-13090800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr18:13073000-13093200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr18:13073200-13090600	Weak transcription	Brain Angular Gyrus	brain
17	chr18:13073200-13090600	Weak transcription	Brain Substantia Nigra	brain
18	chr18:13073400-13090600	Weak transcription	Fetal Kidney	kidney
19	chr18:13073400-13093800	Weak transcription	Fetal Heart	heart
20	chr18:13073400-13094000	Weak transcription	NHLF	lung
21	chr18:13074000-13090600	Weak transcription	Aorta	Aorta
22	chr18:13074200-13087600	Weak transcription	NHDF-Ad	bronchial
23	chr18:13074200-13089400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr18:13074200-13090600	Weak transcription	HSMMtube	muscle
25	chr18:13075000-13089600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr18:13075200-13089600	Weak transcription	HUVEC	blood vessel
27	chr18:13075200-13094400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr18:13075400-13087600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr18:13075400-13090600	Weak transcription	NHEK	skin
30	chr18:13075400-13105400	Weak transcription	Psoas Muscle	Psoas
31	chr18:13075800-13090800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr18:13075800-13095600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr18:13076000-13083000	Weak transcription	Fetal Intestine Large	intestine
34	chr18:13076000-13083200	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr18:13076000-13083200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr18:13076000-13083800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr18:13076000-13083800	Weak transcription	Fetal Lung	lung
38	chr18:13076000-13083800	Weak transcription	Spleen	Spleen
39	chr18:13076000-13084000	Weak transcription	Gastric	stomach
40	chr18:13076000-13084200	Weak transcription	Placenta	Placenta
41	chr18:13076000-13086000	Weak transcription	Primary B cells from cord blood	blood
42	chr18:13076000-13086400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr18:13076000-13086400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr18:13076000-13086600	Weak transcription	Osteobl	bone
45	chr18:13076000-13087000	Weak transcription	HMEC	breast
46	chr18:13076000-13087000	Weak transcription	HSMM	muscle
47	chr18:13076000-13089600	Weak transcription	K562	blood
48	chr18:13076000-13090600	Weak transcription	Colon Smooth Muscle	Colon
49	chr18:13076000-13090800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr18:13076200-13083400	Weak transcription	Duodenum Mucosa	Duodenum

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