Variant report

Variant	rs12955780
Chromosome Location	chr18:12982760-12982761
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12977407..12979654-chr18:12980274..12984512,3	K562	blood:

Variant related genes	Relation type
ENSG00000085415	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10221326	0.85[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10221384	0.81[CEU][hapmap];0.82[MEX][hapmap];0.82[EUR][1000 genomes]
rs11080620	1.00[ASW][hapmap];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];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11663049	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12605638	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12954256	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1474043	1.00[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1786263	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1786270	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1786279	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1787000	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1787003	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1787004	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1787008	1.00[ASW][hapmap];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];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1973779	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28619103	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28641764	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2902856	1.00[ASW][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35790309	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3809912	1.00[ASW][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs472702	0.81[CEU][hapmap];0.82[MEX][hapmap];0.80[EUR][1000 genomes]
rs472992	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs473580	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs474337	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs475139	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs478006	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs478399	0.81[EUR][1000 genomes]
rs482360	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs482577	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs490853	0.94[AMR][1000 genomes]
rs491349	0.81[EUR][1000 genomes]
rs492723	0.83[EUR][1000 genomes]
rs498685	0.80[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4995995	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs518145	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs527839	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs529620	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs547084	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs554719	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs554854	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs556371	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs556536	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs557846	0.84[EUR][1000 genomes]
rs562151	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]
rs565832	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs567031	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs569453	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs570505	1.00[ASW][hapmap];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]
rs576963	0.88[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs578208	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]
rs6505775	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6505776	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6505777	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6505780	1.00[ASW][hapmap];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];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs692833	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs692964	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71353243	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7226616	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7229870	0.82[ASW][hapmap];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];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7233600	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7233814	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7234094	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7234960	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7236162	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7236764	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7237236	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7241536	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7243660	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8088313	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[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];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8089123	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8097038	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8097125	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9783859	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9783903	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9948139	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9948681	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9949589	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9949682	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9951698	0.86[AMR][1000 genomes]
rs9952698	0.82[EUR][1000 genomes]
rs9958369	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9961669	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9964466	1.00[ASW][hapmap];0.92[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];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9965977	0.82[EUR][1000 genomes];0.85[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs12955780	CEP192	cis	Whole Blood	GTEx
rs12955780	CEP192	cis	Stomach	GTEx
rs12955780	SEH1L	cis	parietal	SCAN
rs12955780	CEP192	cis	multi-tissue	Pritchard
rs12955780	CEP192	cis	Esophagus Mucosa	GTEx
rs12955780	CEP192	cis	Artery Tibial	GTEx
rs12955780	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs12955780	CEP192	cis	Nerve Tibial	GTEx
rs12955780	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs12955780	CEP192	cis	parietal	SCAN
rs12955780	CEP192	cis	Adipose Subcutaneous	GTEx
rs12955780	CEP192	cis	Esophagus Muscularis	GTEx
rs12955780	CEP192	cis	cerebellum	SCAN
rs12955780	CEP192	cis	lung	GTEx
rs12955780	CEP192	cis	Thyroid	GTEx
rs12955780	CEP192	cis	Artery Aorta	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12948800-12989000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr18:12949200-12989400	Weak transcription	Psoas Muscle	Psoas
3	chr18:12950000-12990200	Weak transcription	Fetal Brain Male	brain
4	chr18:12951400-12990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr18:12951600-12988200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr18:12959000-12990200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr18:12968600-12983000	Weak transcription	HUVEC	blood vessel
8	chr18:12972800-12990000	Weak transcription	Brain Substantia Nigra	brain
9	chr18:12973200-12983400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr18:12973200-12990200	Weak transcription	Small Intestine	intestine
11	chr18:12974200-12990200	Weak transcription	Brain Hippocampus Middle	brain
12	chr18:12975800-12990200	Weak transcription	Right Ventricle	heart
13	chr18:12976000-12990200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr18:12976200-12983000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr18:12976200-12984000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr18:12976400-12982800	Weak transcription	A549	lung
17	chr18:12976400-12983000	Weak transcription	Colonic Mucosa	Colon
18	chr18:12976400-12983000	Weak transcription	Left Ventricle	heart
19	chr18:12976400-12990000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr18:12976400-12990000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr18:12976400-12990000	Weak transcription	Colon Smooth Muscle	Colon
22	chr18:12976400-12990000	Weak transcription	Stomach Mucosa	stomach
23	chr18:12976400-12990200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr18:12976400-12990200	Weak transcription	Brain Angular Gyrus	brain
25	chr18:12976400-12990200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr18:12976400-12990200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr18:12976400-12990400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr18:12976600-12982800	Weak transcription	Fetal Brain Female	brain
29	chr18:12976600-12982800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr18:12976600-12983000	Weak transcription	Gastric	stomach
31	chr18:12976600-12983000	Weak transcription	Ovary	ovary
32	chr18:12976600-12990000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr18:12976600-12990000	Weak transcription	Fetal Heart	heart
34	chr18:12976600-12990200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr18:12976600-12990200	Weak transcription	Brain Anterior Caudate	brain
36	chr18:12976600-12990200	Weak transcription	Esophagus	oesophagus
37	chr18:12976600-12990200	Weak transcription	Spleen	Spleen
38	chr18:12976600-12990400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr18:12976600-12990800	Weak transcription	Aorta	Aorta
40	chr18:12976800-12983000	Weak transcription	Brain Germinal Matrix	brain
41	chr18:12976800-12990200	Weak transcription	Fetal Lung	lung
42	chr18:12977200-12983000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr18:12977400-12990600	Weak transcription	HSMMtube	muscle
44	chr18:12978000-12985000	Weak transcription	NHDF-Ad	bronchial
45	chr18:12978400-12982800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr18:12978600-12982800	Weak transcription	Fetal Stomach	stomach
47	chr18:12978600-12982800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr18:12978600-12989200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr18:12978600-12990200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr18:12978600-12990200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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