Variant report

Variant	rs1790120
Chromosome Location	chr12:123613565-123613566
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123613552..123616142-chr12:123624690..123626588,2	K562	blood:
2	chr12:123610238..123613639-chr12:123613854..123616666,3	K562	blood:

Extended variants
information (count: 106 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1047158	0.89[EUR][1000 genomes]
rs1051431	0.87[EUR][1000 genomes]
rs10744147	0.85[EUR][1000 genomes]
rs10772993	0.87[EUR][1000 genomes]
rs10772995	0.82[EUR][1000 genomes]
rs10846478	0.82[EUR][1000 genomes]
rs11057192	0.83[EUR][1000 genomes]
rs1106240	0.89[EUR][1000 genomes]
rs1106241	0.88[EUR][1000 genomes]
rs1260294	0.86[EUR][1000 genomes]
rs1402274	0.84[EUR][1000 genomes]
rs1569068	0.87[EUR][1000 genomes]
rs1615694	0.81[EUR][1000 genomes]
rs1616131	0.90[EUR][1000 genomes]
rs1616181	0.90[EUR][1000 genomes]
rs1617156	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1617434	0.88[EUR][1000 genomes]
rs1618679	0.85[EUR][1000 genomes]
rs1621194	0.87[EUR][1000 genomes]
rs1626899	0.81[EUR][1000 genomes]
rs1627724	0.89[EUR][1000 genomes]
rs1630693	0.81[EUR][1000 genomes]
rs1630905	0.82[EUR][1000 genomes]
rs1716156	0.81[EUR][1000 genomes]
rs1716157	0.82[EUR][1000 genomes]
rs1716159	0.82[EUR][1000 genomes]
rs1716160	0.83[EUR][1000 genomes]
rs1716165	0.87[EUR][1000 genomes]
rs1716167	0.87[EUR][1000 genomes]
rs1716168	0.87[EUR][1000 genomes]
rs1716175	0.82[EUR][1000 genomes]
rs1716176	0.85[EUR][1000 genomes]
rs1716177	0.85[EUR][1000 genomes]
rs1716182	0.81[EUR][1000 genomes]
rs1716185	0.87[EUR][1000 genomes]
rs1727290	0.85[EUR][1000 genomes]
rs1727294	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1727296	0.87[EUR][1000 genomes]
rs1727306	0.82[EUR][1000 genomes]
rs1727309	0.83[EUR][1000 genomes]
rs1727310	0.83[EUR][1000 genomes]
rs1727313	0.88[EUR][1000 genomes]
rs1727314	0.87[EUR][1000 genomes]
rs1727315	0.89[EUR][1000 genomes]
rs1727316	0.90[EUR][1000 genomes]
rs1727317	0.90[EUR][1000 genomes]
rs1727318	0.86[EUR][1000 genomes]
rs1727320	0.83[EUR][1000 genomes]
rs1727322	0.83[EUR][1000 genomes]
rs1727323	0.83[EUR][1000 genomes]
rs1727324	0.83[EUR][1000 genomes]
rs1727325	0.83[EUR][1000 genomes]
rs1790086	0.82[EUR][1000 genomes]
rs1790087	0.82[EUR][1000 genomes]
rs1790089	0.84[EUR][1000 genomes]
rs1790090	0.89[EUR][1000 genomes]
rs1790095	0.84[EUR][1000 genomes]
rs1790098	0.85[EUR][1000 genomes]
rs1790100	0.84[EUR][1000 genomes]
rs1790101	0.81[EUR][1000 genomes]
rs1790102	0.81[EUR][1000 genomes]
rs1790108	0.89[EUR][1000 genomes]
rs1790109	0.89[EUR][1000 genomes]
rs1790116	0.90[EUR][1000 genomes]
rs1790119	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1790123	0.83[EUR][1000 genomes]
rs1790130	0.81[EUR][1000 genomes]
rs1790131	0.82[EUR][1000 genomes]
rs2049114	0.82[EUR][1000 genomes]
rs2270789	0.86[ASN][1000 genomes]
rs2510885	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2682429	0.89[EUR][1000 genomes]
rs2682430	0.81[EUR][1000 genomes]
rs2682431	0.83[EUR][1000 genomes]
rs2682433	0.83[EUR][1000 genomes]
rs2682434	0.83[EUR][1000 genomes]
rs2695476	0.83[EUR][1000 genomes]
rs2695478	0.85[EUR][1000 genomes]
rs2695479	0.83[EUR][1000 genomes]
rs2695480	0.82[EUR][1000 genomes]
rs2695481	0.89[EUR][1000 genomes]
rs2695482	0.88[EUR][1000 genomes]
rs2851435	0.81[EUR][1000 genomes]
rs2851438	0.89[EUR][1000 genomes]
rs2851441	0.87[EUR][1000 genomes]
rs2851450	0.83[EUR][1000 genomes]
rs2851451	0.82[EUR][1000 genomes]
rs2947099	0.81[EUR][1000 genomes]
rs2950537	0.81[EUR][1000 genomes]
rs3018098	0.85[EUR][1000 genomes]
rs4372492	0.83[EUR][1000 genomes]
rs520088	0.86[ASN][1000 genomes]
rs585522	0.81[ASN][1000 genomes]
rs655293	0.89[ASN][1000 genomes]
rs71444568	0.85[ASN][1000 genomes]
rs7299943	0.92[ASN][1000 genomes]
rs7975763	0.82[ASN][1000 genomes]
rs884548	0.89[EUR][1000 genomes]
rs949142	0.89[EUR][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	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv870326	chr12:123585990-123719323	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	esv3405030	chr12:123610199-123614397	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1790120	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1790120	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1790120	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1790120	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1790120	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1790120	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs1790120	RP11-282O18.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123594600-123634000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:123599200-123624600	Weak transcription	Fetal Brain Female	brain
3	chr12:123601600-123615800	Weak transcription	Pancreas	Pancrea
4	chr12:123605000-123616000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:123605800-123614200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:123605800-123624400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:123606000-123614600	Weak transcription	Colonic Mucosa	Colon
8	chr12:123607600-123619600	Genic enhancers	Fetal Thymus	thymus
9	chr12:123608000-123614200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr12:123608400-123614200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr12:123610000-123620400	Enhancers	Placenta	Placenta
12	chr12:123610600-123614400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:123611000-123617400	Enhancers	Primary B cells from cord blood	blood
14	chr12:123611200-123614600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:123611400-123616200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:123611400-123624400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:123611600-123614000	Weak transcription	Primary T cells from cord blood	blood
18	chr12:123611600-123614200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr12:123611600-123615800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:123611600-123616200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:123611600-123616600	Weak transcription	Liver	Liver
22	chr12:123611600-123617400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:123611800-123615200	Weak transcription	Fetal Heart	heart
24	chr12:123611800-123615400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr12:123611800-123615600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:123611800-123615800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:123611800-123615800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:123611800-123615800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:123611800-123616000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:123611800-123616000	Weak transcription	Brain Angular Gyrus	brain
31	chr12:123611800-123616200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:123611800-123616200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:123611800-123616200	Weak transcription	Psoas Muscle	Psoas
34	chr12:123611800-123616200	Weak transcription	Small Intestine	intestine
35	chr12:123611800-123616600	Weak transcription	GM12878-XiMat	blood
36	chr12:123611800-123618000	Enhancers	A549	lung
37	chr12:123611800-123624400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:123611800-123624400	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:123611800-123624600	Weak transcription	Aorta	Aorta
40	chr12:123612000-123613600	Enhancers	Thymus	Thymus
41	chr12:123612000-123614400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:123612000-123614600	Weak transcription	Esophagus	oesophagus
43	chr12:123612000-123614600	Weak transcription	Fetal Intestine Large	intestine
44	chr12:123612000-123614800	Weak transcription	Left Ventricle	heart
45	chr12:123612000-123615400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:123612000-123615400	Weak transcription	Lung	lung
47	chr12:123612000-123615400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr12:123612000-123615400	Weak transcription	Hela-S3	cervix
49	chr12:123612000-123615600	Weak transcription	Right Ventricle	heart
50	chr12:123612000-123616000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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