Variant report

Variant	rs12729917
Chromosome Location	chr1:45304406-45304407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
2	chr1:45239193..45241536-chr1:45303716..45305875,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142937	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11211036	0.90[ASN][1000 genomes]
rs11211038	0.88[ASN][1000 genomes]
rs11211040	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211045	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211048	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211051	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11211053	0.86[EUR][1000 genomes]
rs1140279	0.81[ASN][1000 genomes]
rs11573542	0.94[ASN][1000 genomes]
rs11573557	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11573559	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11573562	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11573592	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11584440	0.89[ASN][1000 genomes]
rs11806832	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11809931	0.83[ASN][1000 genomes]
rs12139143	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12569156	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12723764	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12732939	0.81[ASN][1000 genomes]
rs12733586	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12735038	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12738360	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12741443	0.81[ASN][1000 genomes]
rs12746270	0.81[ASN][1000 genomes]
rs16832227	0.81[ASN][1000 genomes]
rs16832263	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16832265	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17881698	0.89[ASN][1000 genomes]
rs17883049	0.89[ASN][1000 genomes]
rs17886118	0.89[ASN][1000 genomes]
rs2295997	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2295998	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2295999	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34436945	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34506400	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34541568	0.82[ASN][1000 genomes]
rs34639510	0.87[ASN][1000 genomes]
rs34984079	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35343809	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35957134	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3795713	0.81[ASN][1000 genomes]
rs3795714	0.81[ASN][1000 genomes]
rs3795719	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4342887	0.81[ASN][1000 genomes]
rs6429549	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6429550	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6676749	0.87[ASN][1000 genomes]
rs6689911	0.81[ASN][1000 genomes]
rs6692487	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6697153	0.83[ASN][1000 genomes]
rs6703452	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67408784	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7517439	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7517639	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7527787	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7528461	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7531019	0.85[EUR][1000 genomes];0.81[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	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
8	nsv546146	chr1:45258141-45318752	Genic enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	109 gene(s)	inside rSNPs	diseases
9	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
10	nsv532505	chr1:45303803-45307152	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12729917	UROD	cis	Artery Tibial	GTEx
rs12729917	UROD	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45286400-45308400	Weak transcription	Aorta	Aorta
2	chr1:45287200-45307400	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:45289400-45307600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:45292400-45308200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:45294000-45308200	Weak transcription	Gastric	stomach
6	chr1:45295400-45308400	Weak transcription	Right Ventricle	heart
7	chr1:45295800-45305600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:45295800-45308000	Weak transcription	Brain Germinal Matrix	brain
9	chr1:45296000-45307600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:45297000-45305200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:45297000-45305200	Weak transcription	Ovary	ovary
12	chr1:45297400-45305200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:45298000-45305200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:45298000-45305400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:45298000-45308200	Weak transcription	Spleen	Spleen
16	chr1:45298200-45305200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:45298800-45308200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:45301800-45305200	Weak transcription	Fetal Lung	lung
19	chr1:45301800-45307400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:45302000-45305200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:45302000-45305200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:45302000-45305200	Weak transcription	Fetal Brain Male	brain
23	chr1:45302000-45306400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:45302000-45307200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:45302000-45307400	Weak transcription	Brain Anterior Caudate	brain
26	chr1:45302000-45307400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:45302000-45307600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:45302000-45307600	Weak transcription	K562	blood
29	chr1:45302000-45308200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:45302000-45308200	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:45302000-45308200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:45302000-45308200	Weak transcription	NHDF-Ad	bronchial
33	chr1:45302000-45308200	Weak transcription	Osteobl	bone
34	chr1:45302000-45308400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:45302000-45308400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:45302000-45308400	Weak transcription	HUVEC	blood vessel
37	chr1:45302200-45304600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr1:45302200-45304600	Weak transcription	Fetal Muscle Leg	muscle
39	chr1:45302200-45305200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:45302200-45305200	Weak transcription	Fetal Brain Female	brain
41	chr1:45302200-45307200	Weak transcription	Brain Angular Gyrus	brain
42	chr1:45302200-45308200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:45302400-45304600	Strong transcription	Fetal Stomach	stomach
44	chr1:45302400-45307600	Weak transcription	Fetal Intestine Small	intestine
45	chr1:45302400-45308400	Weak transcription	Right Atrium	heart
46	chr1:45302600-45307200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:45302800-45307800	Weak transcription	Fetal Kidney	kidney
48	chr1:45302800-45308200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr1:45302800-45308200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:45302800-45308200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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