Variant report

Variant	rs11578233
Chromosome Location	chr1:45201795-45201796
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45195070..45199174-chr1:45199435..45202619,4	MCF-7	breast:
2	chr1:45201048..45202989-chr1:45204988..45207137,2	MCF-7	breast:
3	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
4	chr1:45200496..45202842-chr1:45475554..45478317,2	K562	blood:
5	chr1:45201529..45203868-chr1:46049676..46051618,2	K562	blood:
6	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:
7	chr1:45199496..45202300-chr1:45202425..45207135,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222009	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000173846	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11211025	0.85[EUR][1000 genomes]
rs11211026	0.85[EUR][1000 genomes]
rs11211036	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11211038	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11211040	0.83[ASN][1000 genomes]
rs11211045	0.81[ASN][1000 genomes]
rs11211048	0.81[ASN][1000 genomes]
rs1140279	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11573542	0.80[ASN][1000 genomes]
rs11573592	0.83[ASN][1000 genomes]
rs11580010	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580159	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11582718	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584440	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11800505	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11801990	0.95[ASN][1000 genomes]
rs11803622	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11806832	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11809931	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12566610	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12569156	0.81[ASN][1000 genomes]
rs12723764	0.81[ASN][1000 genomes]
rs12732939	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12733586	0.80[ASN][1000 genomes]
rs12733796	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12735038	0.81[ASN][1000 genomes]
rs12735728	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12738360	0.81[ASN][1000 genomes]
rs12741443	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12746270	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12746898	0.83[EUR][1000 genomes]
rs16832227	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16832265	0.81[ASN][1000 genomes]
rs17881698	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17883049	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17886118	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2295997	0.83[ASN][1000 genomes]
rs2295998	0.82[ASN][1000 genomes]
rs2295999	0.83[ASN][1000 genomes]
rs34541568	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34639510	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34984079	0.82[ASN][1000 genomes]
rs35343809	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35932693	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35957134	0.81[ASN][1000 genomes]
rs3795713	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3795714	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3795719	0.83[ASN][1000 genomes]
rs3820586	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4342887	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57995027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59366549	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59788723	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6429549	0.82[ASN][1000 genomes]
rs6429550	0.81[ASN][1000 genomes]
rs6670449	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6676749	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6689911	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6692487	0.81[ASN][1000 genomes]
rs6695350	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6697153	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6702415	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6704436	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67408784	0.82[ASN][1000 genomes]
rs67742332	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7517439	0.81[ASN][1000 genomes]
rs7517639	0.81[ASN][1000 genomes]
rs7527787	0.82[ASN][1000 genomes]
rs7528461	0.81[ASN][1000 genomes]
rs7534487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536078	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7539538	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7546285	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[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
rs11578233	UROD	cis	Artery Tibial	GTEx
rs11578233	UROD	cis	lung	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45189800-45205000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:45196400-45204200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:45197000-45203800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:45197000-45204200	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:45197000-45204800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:45197000-45204800	Weak transcription	Right Atrium	heart
7	chr1:45197200-45204800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:45197200-45204800	Weak transcription	Fetal Lung	lung
9	chr1:45197600-45204600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:45197600-45204600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:45197600-45204600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:45197600-45204800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:45197600-45204800	Weak transcription	Adipose Nuclei	Adipose
14	chr1:45197800-45203800	Weak transcription	Thymus	Thymus
15	chr1:45197800-45204600	Weak transcription	Primary T cells from cord blood	blood
16	chr1:45197800-45204600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:45197800-45204800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:45197800-45204800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:45197800-45204800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:45197800-45204800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:45197800-45204800	Weak transcription	NH-A	brain
22	chr1:45198000-45204600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:45198000-45204600	Weak transcription	Hela-S3	cervix
24	chr1:45198000-45204800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:45198000-45204800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:45198000-45205000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:45199200-45204800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:45199400-45204000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:45199400-45204200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:45199400-45204800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:45199400-45204800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:45199400-45204800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:45199400-45204800	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:45199400-45204800	Weak transcription	HMEC	breast
35	chr1:45199600-45204800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:45199600-45204800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:45199600-45204800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:45199600-45204800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:45199600-45204800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:45199600-45204800	Weak transcription	NHDF-Ad	bronchial
41	chr1:45199800-45203800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:45199800-45204200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:45199800-45204800	Weak transcription	Osteobl	bone
44	chr1:45200600-45204800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:45200800-45204600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr1:45201000-45204800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr1:45201000-45204800	Weak transcription	HepG2	liver
48	chr1:45201600-45204800	Weak transcription	Placenta	Placenta

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