Variant report

Variant	rs1790088
Chromosome Location	chr12:123673258-123673259
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1051434	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10848428	0.82[AMR][1000 genomes]
rs11057189	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11610710	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11613128	0.89[AFR][1000 genomes]
rs12229700	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1568428	0.82[AFR][1000 genomes]
rs1611973	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1616484	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1626703	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1716178	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1716184	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1727286	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727293	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1727295	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1727301	0.95[ASN][1000 genomes]
rs1727305	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1727312	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1790094	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1790096	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790104	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790106	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1790121	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1790122	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1790129	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1790134	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1879379	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2102949	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2337630	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2337631	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2682427	0.95[ASN][1000 genomes]
rs34841857	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs36121382	0.81[ASN][1000 genomes]
rs3759111	0.82[ASN][1000 genomes]
rs3759113	0.80[ASN][1000 genomes]
rs4148862	0.80[EUR][1000 genomes]
rs4148863	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4460848	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4759406	0.83[ASN][1000 genomes]
rs4759407	0.82[ASN][1000 genomes]
rs60296110	0.83[ASN][1000 genomes]
rs7139321	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73231928	0.83[ASN][1000 genomes]
rs949143	0.89[AMR][1000 genomes];0.82[EUR][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	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
2	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
3	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
4	esv2761773	chr12:123616003-123723460	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers 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 target site	53 gene(s)	inside rSNPs	diseases
5	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1790088	SETD8	Cis_1M	lymphoblastoid	RTeQTL
rs1790088	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1790088	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1790088	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1790088	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1790088	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1790088	RP11-282O18.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123636600-123676200	Weak transcription	Gastric	stomach
2	chr12:123636600-123716600	Weak transcription	Esophagus	oesophagus
3	chr12:123636800-123675200	Weak transcription	Fetal Heart	heart
4	chr12:123636800-123679600	Weak transcription	Colonic Mucosa	Colon
5	chr12:123636800-123687400	Weak transcription	Psoas Muscle	Psoas
6	chr12:123637000-123673400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:123637000-123713000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:123637200-123716400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:123638600-123687200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:123638800-123685000	Strong transcription	Fetal Thymus	thymus
11	chr12:123640400-123676000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:123648400-123679200	Strong transcription	Thymus	Thymus
13	chr12:123648800-123673600	Weak transcription	HMEC	breast
14	chr12:123650400-123686400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:123650600-123673600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:123650600-123685800	Weak transcription	Small Intestine	intestine
17	chr12:123650600-123687200	Weak transcription	Pancreas	Pancrea
18	chr12:123650600-123716400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr12:123651200-123673600	Weak transcription	Brain Substantia Nigra	brain
20	chr12:123651400-123673600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:123651400-123673600	Weak transcription	NHEK	skin
22	chr12:123651400-123675800	Weak transcription	Ovary	ovary
23	chr12:123651600-123676000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr12:123652200-123676200	Weak transcription	Right Ventricle	heart
25	chr12:123652800-123707800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:123654000-123707000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:123654200-123712000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:123654200-123715400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:123654600-123683000	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:123655000-123681000	Strong transcription	Fetal Muscle Trunk	muscle
31	chr12:123655000-123707200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:123655000-123708000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:123655000-123712000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:123655200-123682200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:123657000-123680600	Strong transcription	Fetal Stomach	stomach
36	chr12:123657000-123680800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:123658600-123682000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:123658800-123673600	Weak transcription	NHLF	lung
39	chr12:123658800-123675800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr12:123659000-123673400	Weak transcription	HSMMtube	muscle
41	chr12:123659800-123675200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr12:123661200-123673400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr12:123661400-123673400	Weak transcription	HSMM	muscle
44	chr12:123661400-123687200	Weak transcription	Fetal Brain Male	brain
45	chr12:123663200-123677800	Weak transcription	Colon Smooth Muscle	Colon
46	chr12:123664200-123678000	Weak transcription	Fetal Kidney	kidney
47	chr12:123664600-123673600	Weak transcription	Brain Hippocampus Middle	brain
48	chr12:123664600-123675200	Weak transcription	Placenta	Placenta
49	chr12:123665000-123685800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr12:123665200-123673600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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