Variant report

Variant	rs12733796
Chromosome Location	chr1:45209398-45209399
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45208420-45209731	K562	blood:	n/a	n/a
2	POLR2A	chr1:45209060-45209463	K562	blood:	n/a	n/a
3	POLR2A	chr1:45208368-45209626	K562	blood:	n/a	n/a
4	POLR2A	chr1:45208394-45209435	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45207667..45210587-chr1:45241224..45243801,2	MCF-7	breast:
2	chr1:45202642..45205441-chr1:45208047..45209564,2	MCF-7	breast:
3	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:

Variant related genes	Relation type
KIF2C	TF binding region
ENSG00000225721	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000222009	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

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

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

Chromatin state (count:94 , 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	chr1:45206200-45213400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:45206200-45218400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:45206200-45218800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:45206200-45220000	Weak transcription	Spleen	Spleen
8	chr1:45206200-45224800	Weak transcription	Esophagus	oesophagus
9	chr1:45206200-45225800	Weak transcription	Primary T cells from cord blood	blood
10	chr1:45206200-45227400	Weak transcription	Colonic Mucosa	Colon
11	chr1:45206200-45230200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:45206200-45240400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:45206200-45240600	Weak transcription	Stomach Mucosa	stomach
14	chr1:45206400-45211800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:45206400-45212000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:45206400-45213400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:45206400-45213400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:45206400-45218400	Weak transcription	Gastric	stomach
19	chr1:45206400-45218400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:45206400-45218600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:45206400-45219000	Weak transcription	Primary B cells from cord blood	blood
22	chr1:45206400-45219600	Weak transcription	Placenta	Placenta
23	chr1:45206400-45221400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:45206400-45232800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:45206400-45240600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:45206600-45211600	Weak transcription	Fetal Intestine Small	intestine
27	chr1:45206600-45213000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:45206600-45213400	Weak transcription	Fetal Brain Female	brain
29	chr1:45206600-45240600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:45206800-45210000	Weak transcription	HMEC	breast
31	chr1:45206800-45210800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:45206800-45211800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:45206800-45223000	Weak transcription	Fetal Kidney	kidney
34	chr1:45206800-45226600	Weak transcription	Fetal Brain Male	brain
35	chr1:45206800-45240200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:45207000-45211800	Weak transcription	Fetal Lung	lung
37	chr1:45207000-45216000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:45207000-45218800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:45207000-45233800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:45207200-45210400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:45207200-45234200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr1:45207200-45234400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:45207400-45210400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:45207400-45233800	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:45207600-45233800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:45207600-45234400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:45208200-45212000	Strong transcription	Fetal Thymus	thymus
48	chr1:45208400-45209400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
49	chr1:45208400-45209400	Genic enhancers	HepG2	liver
50	chr1:45208400-45210400	Strong transcription	Fetal Muscle Leg	muscle

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