Variant report

Variant	rs12566610
Chromosome Location	chr1:45216038-45216039
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45213736..45216686-chr1:45219753..45221746,2	MCF-7	breast:
2	chr1:45194641..45196649-chr1:45215211..45217632,2	MCF-7	breast:
3	chr1:45205062..45207058-chr1:45214286..45216582,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142945	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs11211025	0.85[EUR][1000 genomes]
rs11211026	0.85[EUR][1000 genomes]
rs11211036	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211038	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211040	0.84[ASN][1000 genomes]
rs11211045	0.83[ASN][1000 genomes]
rs11211048	0.83[ASN][1000 genomes]
rs11211051	0.80[ASN][1000 genomes]
rs1140279	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11573542	0.82[ASN][1000 genomes]
rs11573592	0.84[ASN][1000 genomes]
rs11578233	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11580010	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11580159	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11582718	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11584440	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11800505	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11801990	0.93[ASN][1000 genomes]
rs11803622	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11806832	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11809931	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12569156	0.83[ASN][1000 genomes]
rs12723764	0.83[ASN][1000 genomes]
rs12732939	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12733586	0.82[ASN][1000 genomes]
rs12733796	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12735038	0.83[ASN][1000 genomes]
rs12735728	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12738360	0.83[ASN][1000 genomes]
rs12741443	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12746270	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12746898	0.83[EUR][1000 genomes]
rs16832227	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16832265	0.83[ASN][1000 genomes]
rs17881698	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17883049	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17886118	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2295997	0.84[ASN][1000 genomes]
rs2295998	0.84[ASN][1000 genomes]
rs2295999	0.84[ASN][1000 genomes]
rs34541568	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34639510	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34984079	0.84[ASN][1000 genomes]
rs35343809	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35932693	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35957134	0.83[ASN][1000 genomes]
rs3795713	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3795714	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3795719	0.84[ASN][1000 genomes]
rs3820586	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4342887	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57995027	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59366549	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59788723	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6429549	0.84[ASN][1000 genomes]
rs6429550	0.83[ASN][1000 genomes]
rs6670449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676749	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6689911	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6692487	0.83[ASN][1000 genomes]
rs6695350	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697153	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6702415	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704436	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67408784	0.84[ASN][1000 genomes]
rs67742332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517439	0.83[ASN][1000 genomes]
rs7517639	0.83[ASN][1000 genomes]
rs7527787	0.84[ASN][1000 genomes]
rs7528461	0.83[ASN][1000 genomes]
rs7534487	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7536078	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7539538	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7546285	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	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
7	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
rs12566610	UROD	cis	Artery Tibial	GTEx
rs12566610	UROD	cis	lung	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45205800-45240600	Weak transcription	Ovary	ovary
2	chr1:45206000-45223400	Weak transcription	Lung	lung
3	chr1:45206000-45240400	Weak transcription	Right Atrium	heart
4	chr1:45206200-45218400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:45206200-45218800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:45206200-45220000	Weak transcription	Spleen	Spleen
7	chr1:45206200-45224800	Weak transcription	Esophagus	oesophagus
8	chr1:45206200-45225800	Weak transcription	Primary T cells from cord blood	blood
9	chr1:45206200-45227400	Weak transcription	Colonic Mucosa	Colon
10	chr1:45206200-45230200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:45206200-45240400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:45206200-45240600	Weak transcription	Stomach Mucosa	stomach
13	chr1:45206400-45218400	Weak transcription	Gastric	stomach
14	chr1:45206400-45218400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:45206400-45218600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:45206400-45219000	Weak transcription	Primary B cells from cord blood	blood
17	chr1:45206400-45219600	Weak transcription	Placenta	Placenta
18	chr1:45206400-45221400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:45206400-45232800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:45206400-45240600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:45206600-45240600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:45206800-45223000	Weak transcription	Fetal Kidney	kidney
23	chr1:45206800-45226600	Weak transcription	Fetal Brain Male	brain
24	chr1:45206800-45240200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:45207000-45218800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:45207000-45233800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:45207200-45234200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr1:45207200-45234400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:45207400-45233800	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:45207600-45233800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:45207600-45234400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:45208400-45216600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr1:45208600-45233400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:45208600-45234000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:45208800-45234400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:45209000-45218400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:45209200-45218600	Weak transcription	Brain Germinal Matrix	brain
38	chr1:45209200-45221600	Weak transcription	Fetal Heart	heart
39	chr1:45209400-45216800	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:45209400-45235200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:45209800-45216600	Strong transcription	Hela-S3	cervix
42	chr1:45211000-45216800	Strong transcription	Dnd41	blood
43	chr1:45211200-45233800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:45211400-45218600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:45211400-45229400	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr1:45211400-45233600	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr1:45211400-45234800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:45211400-45235000	Strong transcription	Fetal Stomach	stomach
49	chr1:45211600-45216400	Strong transcription	Fetal Intestine Small	intestine
50	chr1:45211600-45216800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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