Variant report

Variant	rs12150991
Chromosome Location	chr19:18688027-18688028
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18678376..18688390-chr19:18697032..18707656,34	K562	blood:
2	chr19:18668375..18670644-chr19:18686525..18688887,2	K562	blood:
3	chr19:18686406..18688359-chr19:18794458..18796312,2	K562	blood:
4	chr19:18685737..18689884-chr19:18697340..18702135,5	MCF-7	breast:
5	chr19:18685970..18689439-chr19:18690944..18695066,3	MCF-7	breast:
6	chr19:18666982..18671000-chr19:18686640..18690088,4	K562	blood:

Variant related genes	Relation type
ENSG00000006015	Chromatin interaction
ENSG00000006016	Chromatin interaction
ENSG00000105662	Chromatin interaction
ENSG00000105700	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10402321	0.85[EUR][1000 genomes]
rs10409392	0.83[EUR][1000 genomes]
rs10414427	0.85[EUR][1000 genomes]
rs10425018	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11086114	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11086116	0.81[ASN][1000 genomes]
rs11667551	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672297	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12608925	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12609505	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1468475	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2057649	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2058077	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2079015	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2079016	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2283616	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2302055	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2314664	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2314665	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2314666	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2314667	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28451415	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28711754	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35867875	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35875334	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36050418	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3761034	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761036	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3803917	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4629093	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808137	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808821	0.91[ASN][1000 genomes]
rs55724121	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55888366	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58782998	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59798925	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62137086	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7247557	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7253088	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7254004	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7258480	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7648	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription 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 miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
6	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv911283	chr19:18626732-18689830	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
9	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12150991	UBA52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18684200-18688800	Strong transcription	H9 Cell Line	embryonic stem cell
2	chr19:18684200-18688800	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr19:18684200-18689400	Weak transcription	Fetal Heart	heart
4	chr19:18684200-18690200	Strong transcription	Fetal Brain Female	brain
5	chr19:18684400-18688200	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr19:18684400-18688600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr19:18684400-18688800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:18684400-18688800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr19:18684400-18688800	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr19:18684400-18688800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:18684400-18688800	Strong transcription	Thymus	Thymus
12	chr19:18684400-18689000	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr19:18684400-18689200	Strong transcription	Fetal Muscle Trunk	muscle
14	chr19:18684400-18689400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr19:18684400-18689400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:18684400-18689400	Strong transcription	Liver	Liver
17	chr19:18684400-18689600	Strong transcription	Fetal Stomach	stomach
18	chr19:18684400-18689600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr19:18684400-18689800	Strong transcription	Brain Anterior Caudate	brain
20	chr19:18684400-18689800	Strong transcription	Brain Hippocampus Middle	brain
21	chr19:18684400-18689800	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr19:18684400-18690200	Strong transcription	Primary T cells from cord blood	blood
23	chr19:18684400-18691400	Weak transcription	Fetal Brain Male	brain
24	chr19:18684400-18698600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr19:18684600-18688200	Strong transcription	Brain Cingulate Gyrus	brain
26	chr19:18684600-18688400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr19:18684600-18688400	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr19:18684600-18688400	Strong transcription	Colon Smooth Muscle	Colon
29	chr19:18684600-18688400	Strong transcription	Fetal Intestine Large	intestine
30	chr19:18684600-18688600	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:18684600-18688600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr19:18684600-18688600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr19:18684600-18688600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr19:18684600-18688600	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr19:18684600-18688600	Strong transcription	A549	lung
36	chr19:18684600-18688800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:18684600-18688800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:18684600-18688800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr19:18684600-18688800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr19:18684600-18688800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:18684600-18688800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:18684600-18688800	Strong transcription	Brain Germinal Matrix	brain
43	chr19:18684600-18688800	Strong transcription	Gastric	stomach
44	chr19:18684600-18688800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr19:18684600-18688800	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr19:18684600-18688800	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr19:18684600-18688800	Strong transcription	Spleen	Spleen
48	chr19:18684600-18688800	Strong transcription	GM12878-XiMat	blood
49	chr19:18684600-18688800	Strong transcription	NHEK	skin
50	chr19:18684600-18689000	Strong transcription	Duodenum Mucosa	Duodenum

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