Variant report

Variant	rs55888366
Chromosome Location	chr19:18681122-18681123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:18680885-18681231	K562	blood:	n/a	n/a
2	POLR2A	chr19:18680692-18681296	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:18680994-18681164	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr19:18680937-18681396	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr19:18680947-18681367	K562	blood:	n/a	n/a
6	POLR2A	chr19:18680216-18681232	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:18680969-18681353	K562	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18631257..18635225-chr19:18680941..18684038,5	MCF-7	breast:
2	chr19:18629832..18635572-chr19:18680910..18686315,11	K562	blood:
3	chr19:18666965..18674770-chr19:18676405..18685095,25	K562	blood:
4	chr19:18678376..18688390-chr19:18697032..18707656,34	K562	blood:
5	chr19:18651498..18655648-chr19:18680777..18683781,5	MCF-7	breast:
6	chr19:18586402..18589298-chr19:18680966..18684505,3	K562	blood:
7	chr19:18653470..18656783-chr19:18680897..18684291,6	K562	blood:
8	chr19:18681104..18684544-chr19:18745683..18749906,4	K562	blood:
9	chr19:18667097..18671007-chr19:18677068..18684435,17	K562	blood:
10	chr19:18666812..18670172-chr19:18680715..18684041,6	MCF-7	breast:
11	chr19:18628801..18634367-chr19:18680492..18684131,12	MCF-7	breast:
12	chr19:18629832..18634516-chr19:18680910..18685097,11	K562	blood:
13	chr19:18555082..18556968-chr19:18679679..18681810,2	MCF-7	breast:
14	chr19:18651038..18656783-chr19:18680897..18685521,14	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268983	TF binding region
UBA52	TF binding region
ENSG00000006016	Chromatin interaction
ENSG00000105701	Chromatin interaction
ENSG00000167487	Chromatin interaction
ENSG00000105700	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000105656	Chromatin interaction
ENSG00000268030	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10402321	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10409392	0.83[EUR][1000 genomes]
rs10414427	0.85[EUR][1000 genomes]
rs10425018	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11086114	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11086116	0.86[ASN][1000 genomes]
rs11667551	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11672297	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12150991	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12608925	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12609505	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1468475	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2057649	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2058077	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2079015	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2079016	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2283616	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2302055	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2314664	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2314665	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2314666	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2314667	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28451415	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28711754	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28884574	0.81[ASN][1000 genomes]
rs35867875	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35875334	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36050418	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3761034	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3761036	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3803917	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4629093	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4808137	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808821	0.87[ASN][1000 genomes]
rs55724121	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58782998	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59798925	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62137086	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62137090	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6554	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7247557	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7253088	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7254004	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7258480	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7648	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8110371	0.82[ASN][1000 genomes]
rs8110374	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
10	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
rs55888366	UBA52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18669800-18682000	Weak transcription	Fetal Brain Male	brain
2	chr19:18669800-18682200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:18670200-18681200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:18670600-18681200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr19:18670600-18682000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:18671000-18681200	Strong transcription	Fetal Intestine Small	intestine
7	chr19:18671000-18681200	Strong transcription	Fetal Stomach	stomach
8	chr19:18671000-18681400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:18671200-18681200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:18671200-18681200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr19:18671400-18681200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:18672400-18681200	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr19:18672400-18681200	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr19:18672400-18681200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:18672400-18681200	Strong transcription	Dnd41	blood
16	chr19:18672400-18681200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr19:18672600-18681200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:18673000-18681200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:18673200-18681200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:18673400-18681200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:18673400-18681200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr19:18673600-18681200	Strong transcription	Liver	Liver
23	chr19:18673800-18681200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:18673800-18681400	Strong transcription	Fetal Muscle Leg	muscle
25	chr19:18673800-18682000	Weak transcription	Right Atrium	heart
26	chr19:18674200-18681600	Strong transcription	Osteobl	bone
27	chr19:18674400-18681200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:18676000-18682000	Weak transcription	Fetal Kidney	kidney
29	chr19:18678000-18682000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr19:18678400-18682000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr19:18678600-18681800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr19:18678600-18682000	Weak transcription	Psoas Muscle	Psoas
33	chr19:18679400-18681800	Weak transcription	Stomach Mucosa	stomach
34	chr19:18679600-18682000	Weak transcription	A549	lung
35	chr19:18679600-18682000	Weak transcription	NH-A	brain
36	chr19:18679600-18682000	Weak transcription	NHDF-Ad	bronchial
37	chr19:18679600-18682200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:18679800-18681200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr19:18679800-18681800	Weak transcription	Primary B cells from cord blood	blood
40	chr19:18679800-18682000	Weak transcription	Brain Angular Gyrus	brain
41	chr19:18679800-18682000	Weak transcription	Fetal Lung	lung
42	chr19:18679800-18682000	Weak transcription	Hela-S3	cervix
43	chr19:18679800-18682200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr19:18679800-18682200	Weak transcription	Esophagus	oesophagus
45	chr19:18679800-18682600	Weak transcription	Small Intestine	intestine
46	chr19:18680000-18681800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr19:18680000-18682000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr19:18680000-18682000	Weak transcription	HSMMtube	muscle
49	chr19:18680200-18681800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr19:18680200-18682000	Weak transcription	Brain Hippocampus Middle	brain

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