Variant report

Variant	rs12741443
Chromosome Location	chr1:45235755-45235756
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45232158..45236303-chr1:45285320..45287669,3	K562	blood:
2	chr1:45233249..45236557-chr1:45240025..45243176,4	MCF-7	breast:
3	chr1:45231631..45238991-chr1:45243171..45249973,8	K562	blood:

Variant related genes	Relation type
ENSG00000202444	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000234093	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11211036	0.91[ASN][1000 genomes]
rs11211038	0.88[ASN][1000 genomes]
rs11211040	0.86[ASN][1000 genomes]
rs11211045	0.84[ASN][1000 genomes]
rs11211048	0.84[ASN][1000 genomes]
rs11211051	0.82[ASN][1000 genomes]
rs1140279	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11573542	0.84[ASN][1000 genomes]
rs11573557	0.82[ASN][1000 genomes]
rs11573559	0.82[ASN][1000 genomes]
rs11573562	0.82[ASN][1000 genomes]
rs11573592	0.86[ASN][1000 genomes]
rs11578233	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11580010	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11580159	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11582718	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11584440	0.92[ASN][1000 genomes]
rs11800505	0.87[ASN][1000 genomes]
rs11801990	0.90[ASN][1000 genomes]
rs11803622	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11806832	0.89[ASN][1000 genomes]
rs11809931	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12139143	0.81[ASN][1000 genomes]
rs12566610	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12569156	0.84[ASN][1000 genomes]
rs12723764	0.84[ASN][1000 genomes]
rs12729917	0.81[ASN][1000 genomes]
rs12732939	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12733586	0.84[ASN][1000 genomes]
rs12733796	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12735038	0.84[ASN][1000 genomes]
rs12735728	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12738360	0.84[ASN][1000 genomes]
rs12746270	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16832227	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16832263	0.82[ASN][1000 genomes]
rs16832265	0.84[ASN][1000 genomes]
rs17881698	0.92[ASN][1000 genomes]
rs17883049	0.90[ASN][1000 genomes]
rs17886118	0.90[ASN][1000 genomes]
rs2295997	0.86[ASN][1000 genomes]
rs2295998	0.85[ASN][1000 genomes]
rs2295999	0.86[ASN][1000 genomes]
rs34436945	0.82[ASN][1000 genomes]
rs34541568	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34639510	0.94[ASN][1000 genomes]
rs34984079	0.85[ASN][1000 genomes]
rs35343809	0.89[ASN][1000 genomes]
rs35932693	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35957134	0.84[ASN][1000 genomes]
rs3795713	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3795714	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3795719	0.86[ASN][1000 genomes]
rs3820586	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4342887	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57995027	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59366549	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59788723	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6429549	0.85[ASN][1000 genomes]
rs6429550	0.84[ASN][1000 genomes]
rs6670449	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6676749	0.94[ASN][1000 genomes]
rs6689911	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6692487	0.84[ASN][1000 genomes]
rs6695350	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6697153	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6702415	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6703452	0.81[ASN][1000 genomes]
rs6704436	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67408784	0.85[ASN][1000 genomes]
rs67742332	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7517439	0.84[ASN][1000 genomes]
rs7517639	0.84[ASN][1000 genomes]
rs7527787	0.85[ASN][1000 genomes]
rs7528461	0.84[ASN][1000 genomes]
rs7534487	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7536078	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7539538	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7546285	0.84[EUR][1000 genomes];0.94[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	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
8	nsv461406	chr1:45218542-45293518	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
9	nsv546145	chr1:45218542-45293518	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
10	nsv870815	chr1:45233638-45318752	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12741443	UROD	cis	lung	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45205800-45240600	Weak transcription	Ovary	ovary
2	chr1:45206000-45240400	Weak transcription	Right Atrium	heart
3	chr1:45206200-45240400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:45206200-45240600	Weak transcription	Stomach Mucosa	stomach
5	chr1:45206400-45240600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:45206600-45240600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:45206800-45240200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:45214400-45240400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:45218000-45240600	Weak transcription	Small Intestine	intestine
10	chr1:45219200-45240600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:45219200-45240800	Weak transcription	Gastric	stomach
12	chr1:45223800-45240600	Weak transcription	Fetal Heart	heart
13	chr1:45224000-45240400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:45224200-45240400	Weak transcription	Lung	lung
15	chr1:45224800-45240400	Weak transcription	HSMMtube	muscle
16	chr1:45225400-45240000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:45226600-45240400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:45226800-45240600	Weak transcription	Left Ventricle	heart
19	chr1:45227000-45240200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:45228600-45240000	Weak transcription	Colonic Mucosa	Colon
21	chr1:45228600-45240400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:45229200-45240000	Weak transcription	HMEC	breast
23	chr1:45229200-45240400	Weak transcription	Primary T cells from cord blood	blood
24	chr1:45229200-45240400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:45229200-45240400	Weak transcription	Brain Germinal Matrix	brain
26	chr1:45229200-45240600	Weak transcription	Fetal Lung	lung
27	chr1:45229400-45240000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:45229400-45240400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:45229400-45240400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:45229400-45240400	Weak transcription	HSMM	muscle
31	chr1:45229400-45240400	Weak transcription	NH-A	brain
32	chr1:45231600-45240600	Weak transcription	Brain Angular Gyrus	brain
33	chr1:45232600-45240200	Weak transcription	Primary B cells from cord blood	blood
34	chr1:45232600-45240400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:45232800-45240400	Weak transcription	Hela-S3	cervix
36	chr1:45233000-45236400	Weak transcription	HepG2	liver
37	chr1:45233000-45237200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:45233200-45240200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:45233200-45240200	Weak transcription	Spleen	Spleen
40	chr1:45233200-45240400	Weak transcription	GM12878-XiMat	blood
41	chr1:45233200-45240400	Weak transcription	NHEK	skin
42	chr1:45233200-45240600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:45233200-45240600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:45233400-45240200	Weak transcription	Fetal Intestine Small	intestine
45	chr1:45233400-45240400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:45233400-45240400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:45233400-45240400	Weak transcription	Fetal Intestine Large	intestine
48	chr1:45233600-45239600	Weak transcription	K562	blood
49	chr1:45233600-45240200	Weak transcription	Dnd41	blood
50	chr1:45233600-45240400	Weak transcription	H9 Cell Line	embryonic stem cell

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