Variant report

Variant	rs7539538
Chromosome Location	chr1:45200267-45200268
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45190324..45200952-chr1:45272085..45288310,59	MCF-7	breast:
2	chr1:45195070..45199174-chr1:45199435..45202619,4	MCF-7	breast:
3	chr1:45193443..45200768-chr1:45280884..45289784,25	MCF-7	breast:
4	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
5	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:
6	chr1:45199496..45202300-chr1:45202425..45207135,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188396	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000202444	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11211025	0.83[EUR][1000 genomes]
rs11211026	0.83[EUR][1000 genomes]
rs11211036	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11211038	0.81[ASN][1000 genomes]
rs1140279	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11578233	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11580010	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11580159	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11582718	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11584440	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11800505	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11801990	0.91[ASN][1000 genomes]
rs11803622	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11806832	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11809931	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12566610	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12732939	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12733796	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12735728	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12741443	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12746270	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12746898	0.81[EUR][1000 genomes]
rs16832227	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17881698	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17883049	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17886118	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34541568	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34639510	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35343809	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35932693	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3795713	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3795714	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3820586	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4342887	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57995027	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59366549	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59788723	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6670449	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6676749	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6689911	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6695350	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6697153	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6702415	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6704436	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67742332	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7534487	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7536078	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7546285	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[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	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
5	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
6	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
7	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
8	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
9	nsv998871	chr1:45196587-45251179	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	171 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7539538	UROD	cis	lung	GTEx
rs7539538	UROD	cis	Artery Tibial	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45189800-45205000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:45193400-45200400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:45196400-45204200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:45197000-45203800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:45197000-45204200	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:45197000-45204800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:45197000-45204800	Weak transcription	Right Atrium	heart
8	chr1:45197200-45204800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:45197200-45204800	Weak transcription	Fetal Lung	lung
10	chr1:45197600-45204600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:45197600-45204600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:45197600-45204600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:45197600-45204800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:45197600-45204800	Weak transcription	Adipose Nuclei	Adipose
15	chr1:45197800-45200400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:45197800-45200400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr1:45197800-45200400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr1:45197800-45200600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:45197800-45203800	Weak transcription	Thymus	Thymus
20	chr1:45197800-45204600	Weak transcription	Primary T cells from cord blood	blood
21	chr1:45197800-45204600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:45197800-45204800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:45197800-45204800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:45197800-45204800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:45197800-45204800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:45197800-45204800	Weak transcription	NH-A	brain
27	chr1:45198000-45200600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:45198000-45201600	Enhancers	Placenta	Placenta
29	chr1:45198000-45204600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:45198000-45204600	Weak transcription	Hela-S3	cervix
31	chr1:45198000-45204800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:45198000-45204800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:45198000-45205000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:45199200-45204800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:45199400-45200600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:45199400-45204000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:45199400-45204200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:45199400-45204800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:45199400-45204800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:45199400-45204800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:45199400-45204800	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:45199400-45204800	Weak transcription	HMEC	breast
43	chr1:45199600-45204800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:45199600-45204800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:45199600-45204800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:45199600-45204800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:45199600-45204800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr1:45199600-45204800	Weak transcription	NHDF-Ad	bronchial
49	chr1:45199800-45203800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:45199800-45204200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links