Variant report

Variant	rs3761034
Chromosome Location	chr19:18680478-18680479
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:18680263-18680575	K562	blood:	n/a	n/a
2	POLR2A	chr19:18680168-18680541	K562	blood:	n/a	n/a
3	POLR2A	chr19:18679880-18680518	K562	blood:	n/a	n/a
4	POLR2A	chr19:18680216-18681232	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:18680094-18680481	HL-60	blood:	n/a	n/a
6	POLR2A	chr19:18680185-18680582	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18666965..18674770-chr19:18676405..18685095,25	K562	blood:
2	chr19:18678376..18688390-chr19:18697032..18707656,34	K562	blood:
3	chr19:18667097..18671007-chr19:18677068..18684435,17	K562	blood:
4	chr19:18555082..18556968-chr19:18679679..18681810,2	MCF-7	breast:

No data

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

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10402321	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10409392	0.80[CEU][hapmap];0.81[CHB][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs10414427	0.85[EUR][1000 genomes]
rs10425018	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11086114	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11086116	0.85[ASN][1000 genomes]
rs11667551	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11672297	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12150991	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12608925	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12609505	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1468475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2057649	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2058077	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2079015	0.81[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2079016	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2283616	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2302055	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2314664	0.84[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2314665	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2314666	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2314667	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28451415	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28711754	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28884574	0.80[ASN][1000 genomes]
rs35867875	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35875334	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36050418	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3761036	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3803917	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4629093	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808137	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808821	0.86[ASN][1000 genomes]
rs55724121	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55888366	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58782998	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59798925	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62137086	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62137090	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6554	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7247557	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7253088	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7254004	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7258480	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7648	0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8109364	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap]
rs8110371	0.81[ASN][1000 genomes]
rs8110374	0.81[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3761034	UBA52	cis	lymphoblastoid	seeQTL
rs3761034	UBA52	Cis_1M	lymphoblastoid	RTeQTL
rs3761034	NDUFA13	cis	parietal	SCAN

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	chr19:18671200-18680600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr19:18671200-18680600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr19:18671200-18680600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:18671200-18680600	Strong transcription	Fetal Brain Female	brain
13	chr19:18671200-18680600	Strong transcription	Fetal Intestine Large	intestine
14	chr19:18671200-18680600	Strong transcription	Fetal Thymus	thymus
15	chr19:18671200-18681200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:18671200-18681200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr19:18671400-18681200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:18671800-18680600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr19:18671800-18680600	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr19:18672200-18680600	Strong transcription	Brain Germinal Matrix	brain
21	chr19:18672400-18680600	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr19:18672400-18680600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
23	chr19:18672400-18680600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr19:18672400-18680600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr19:18672400-18680600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:18672400-18680600	Strong transcription	Brain Anterior Caudate	brain
27	chr19:18672400-18680600	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr19:18672400-18680600	Strong transcription	Gastric	stomach
29	chr19:18672400-18680600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr19:18672400-18680600	Strong transcription	Thymus	Thymus
31	chr19:18672400-18681000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:18672400-18681000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr19:18672400-18681000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:18672400-18681000	Strong transcription	Primary T cells from cord blood	blood
35	chr19:18672400-18681200	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr19:18672400-18681200	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr19:18672400-18681200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:18672400-18681200	Strong transcription	Dnd41	blood
39	chr19:18672400-18681200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr19:18672600-18680600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr19:18672600-18680600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr19:18672600-18680600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:18672600-18680600	Strong transcription	Rectal Smooth Muscle	rectum
44	chr19:18672600-18680600	Strong transcription	GM12878-XiMat	blood
45	chr19:18672600-18681000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:18672600-18681200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:18672800-18680600	Strong transcription	Pancreas	Pancrea
48	chr19:18672800-18680600	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr19:18673000-18680600	Strong transcription	Spleen	Spleen
50	chr19:18673000-18681200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links