Variant report

Variant	rs1790122
Chromosome Location	chr12:123606739-123606740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123604029..123607309-chr12:123609256..123611485,3	K562	blood:
2	chr12:123606578..123609503-chr12:123615590..123618245,2	MCF-7	breast:
3	chr12:123601823..123603521-chr12:123605557..123608187,2	K562	blood:
4	chr12:123602021..123604363-chr12:123605603..123608187,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1051434	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10773921	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10846489	0.82[AFR][1000 genomes]
rs10848428	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057219	0.82[AFR][1000 genomes]
rs1109559	0.82[AFR][1000 genomes]
rs11608811	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11610710	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11613128	0.87[AFR][1000 genomes]
rs11613937	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12229700	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12425009	0.82[EUR][1000 genomes]
rs12425850	0.82[EUR][1000 genomes]
rs1568428	0.84[AFR][1000 genomes]
rs1611973	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1616484	0.85[AFR][1000 genomes]
rs1626703	0.84[AFR][1000 genomes]
rs1716178	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1716184	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1727286	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1727293	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1727295	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1727305	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1727307	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1727312	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1790088	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1790094	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790096	0.84[AFR][1000 genomes]
rs1790104	0.87[AFR][1000 genomes]
rs1790106	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1790121	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1790129	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1790134	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1879379	0.82[AFR][1000 genomes]
rs1984658	0.81[EUR][1000 genomes]
rs2337630	0.82[AFR][1000 genomes]
rs2337631	0.82[AFR][1000 genomes]
rs28755851	0.80[EUR][1000 genomes]
rs34841857	0.82[AFR][1000 genomes]
rs3741530	0.80[EUR][1000 genomes]
rs4148862	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4148863	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4553407	0.82[AFR][1000 genomes]
rs7135296	0.81[EUR][1000 genomes]
rs7139321	0.87[AFR][1000 genomes]
rs7305511	0.81[EUR][1000 genomes]
rs7957096	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs949143	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1790122	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1790122	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1790122	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1790122	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1790122	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1790122	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123592800-123611200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:123594600-123607200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:123594600-123634000	Weak transcription	Brain Germinal Matrix	brain
4	chr12:123595200-123610800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:123597400-123608200	Enhancers	Primary B cells from peripheral blood	blood
6	chr12:123597800-123610800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr12:123598000-123608400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr12:123599200-123624600	Weak transcription	Fetal Brain Female	brain
9	chr12:123600000-123611200	Weak transcription	Aorta	Aorta
10	chr12:123600600-123610600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:123600600-123610800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:123600600-123610800	Weak transcription	Fetal Intestine Small	intestine
13	chr12:123600600-123610800	Weak transcription	Stomach Mucosa	stomach
14	chr12:123600600-123611000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr12:123600600-123611000	Weak transcription	Small Intestine	intestine
16	chr12:123601000-123610600	Weak transcription	Osteobl	bone
17	chr12:123601400-123611000	Weak transcription	Psoas Muscle	Psoas
18	chr12:123601600-123607400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:123601600-123615800	Weak transcription	Pancreas	Pancrea
20	chr12:123602600-123607200	Weak transcription	Brain Hippocampus Middle	brain
21	chr12:123602800-123610800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:123602800-123610800	Weak transcription	Fetal Heart	heart
23	chr12:123603200-123608400	Enhancers	Primary T cells fromperipheralblood	blood
24	chr12:123603600-123608000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:123604200-123607800	Enhancers	Primary B cells from cord blood	blood
26	chr12:123604400-123608000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:123604400-123608000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr12:123604400-123608000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr12:123604400-123608400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:123604600-123607600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:123604600-123608000	Enhancers	Colon Smooth Muscle	Colon
32	chr12:123604800-123606800	Enhancers	Lung	lung
33	chr12:123604800-123607400	Enhancers	Left Ventricle	heart
34	chr12:123604800-123607800	Enhancers	Brain Anterior Caudate	brain
35	chr12:123605000-123606800	Enhancers	Hela-S3	cervix
36	chr12:123605000-123607200	Enhancers	Liver	Liver
37	chr12:123605000-123607200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:123605000-123616000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:123605200-123607600	Enhancers	A549	lung
40	chr12:123605400-123607000	Enhancers	Primary T cells from cord blood	blood
41	chr12:123605400-123608000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr12:123605400-123610600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:123605600-123608400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr12:123605600-123610800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr12:123605800-123608400	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr12:123605800-123610600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:123605800-123610600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:123605800-123610600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:123605800-123610600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:123605800-123610600	Weak transcription	Fetal Stomach	stomach

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