Variant report

Variant	rs59798925
Chromosome Location	chr19:18671740-18671741
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:18671681-18672071	K562	blood:	n/a	n/a
2	POLR2A	chr19:18671719-18671867	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:18671569-18672200	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18669154..18672917-chr19:18697910..18700793,4	K562	blood:
2	chr19:18630485..18634839-chr19:18666846..18671916,7	MCF-7	breast:
3	chr19:18671310..18673503-chr19:18682435..18684299,2	MCF-7	breast:
4	chr19:18666965..18674770-chr19:18676405..18685095,25	K562	blood:

Variant related genes	Relation type
KXD1	TF binding region
ENSG00000221983	Chromatin interaction
ENSG00000268983	Chromatin interaction
ENSG00000105656	Chromatin interaction
ENSG00000006015	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10402321	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10414427	0.85[EUR][1000 genomes]
rs10425018	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11086114	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11086116	0.93[ASN][1000 genomes]
rs11667551	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11672297	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12150991	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12608925	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12609505	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1468475	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2057649	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2058077	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2079015	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2079016	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2283616	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2302055	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2314664	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2314665	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2314666	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2314667	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28451415	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28711754	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28884574	0.86[ASN][1000 genomes]
rs35867875	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35875334	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36050418	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3761034	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3761036	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3803917	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4629093	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4808137	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4808821	0.89[ASN][1000 genomes]
rs55724121	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55888366	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58782998	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62137086	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6554	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7247557	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7253088	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7254004	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7648	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8110371	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8110374	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv1061733	chr19:18574940-18679155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1055794	chr19:18611545-18676933	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	nsv911284	chr19:18643036-18684216	Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
12	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
rs59798925	UBA52	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18669400-18672400	Weak transcription	Ovary	ovary
2	chr19:18669400-18675600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:18669600-18672400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:18669600-18672400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:18669600-18672400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:18669600-18672400	Weak transcription	Fetal Lung	lung
7	chr19:18669600-18672400	Weak transcription	Gastric	stomach
8	chr19:18669600-18674800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr19:18669600-18675400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:18669600-18675400	Weak transcription	Fetal Kidney	kidney
11	chr19:18669600-18677600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr19:18669800-18671800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:18669800-18671800	Weak transcription	Aorta	Aorta
14	chr19:18669800-18671800	Weak transcription	Brain Hippocampus Middle	brain
15	chr19:18669800-18672200	Weak transcription	Brain Germinal Matrix	brain
16	chr19:18669800-18672400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr19:18669800-18672400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:18669800-18672400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:18669800-18672400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr19:18669800-18672400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr19:18669800-18672400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr19:18669800-18672400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:18669800-18672400	Weak transcription	Brain Angular Gyrus	brain
24	chr19:18669800-18672400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr19:18669800-18672400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:18669800-18672400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr19:18669800-18672400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr19:18669800-18672400	Weak transcription	Left Ventricle	heart
29	chr19:18669800-18672400	Weak transcription	Lung	lung
30	chr19:18669800-18672400	Weak transcription	Right Atrium	heart
31	chr19:18669800-18672600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr19:18669800-18672600	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr19:18669800-18672600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr19:18669800-18672800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr19:18669800-18673600	Weak transcription	Brain Substantia Nigra	brain
36	chr19:18669800-18673800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:18669800-18674000	Weak transcription	NH-A	brain
38	chr19:18669800-18674200	Weak transcription	Esophagus	oesophagus
39	chr19:18669800-18674600	Weak transcription	Small Intestine	intestine
40	chr19:18669800-18675400	Weak transcription	Colon Smooth Muscle	Colon
41	chr19:18669800-18682000	Weak transcription	Fetal Brain Male	brain
42	chr19:18669800-18682200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:18670000-18671800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr19:18670200-18672400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr19:18670200-18672600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:18670200-18675400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr19:18670200-18681200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:18670400-18672400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr19:18670400-18672400	Weak transcription	Brain Anterior Caudate	brain
50	chr19:18670400-18672400	Weak transcription	Thymus	Thymus

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