Variant report

Variant	rs12239165
Chromosome Location	chr1:45490008-45490009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10465876	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749854	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211066	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211067	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11801218	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809982	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118189	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12134146	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12142302	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12143560	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12724597	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12731245	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12735549	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12739545	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12749939	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12755751	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12760109	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13948	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050869	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2236576	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275598	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2275599	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298005	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806405	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6678726	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7514998	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7521339	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7525733	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7535347	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7541207	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7541351	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8681	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs998418	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
5	nsv524385	chr1:45488591-45491504	Weak transcription ZNF genes & repeats Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12239165	UROD	cis	Adipose Subcutaneous	GTEx
rs12239165	UROD	cis	Nerve Tibial	GTEx
rs12239165	UROD	cis	Thyroid	GTEx
rs12239165	UROD	cis	Esophagus Muscularis	GTEx
rs12239165	UROD	cis	Artery Tibial	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45478600-45500000	Weak transcription	Aorta	Aorta
2	chr1:45479000-45493000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:45480800-45500000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:45480800-45500600	Weak transcription	HepG2	liver
5	chr1:45480800-45501200	Weak transcription	Fetal Brain Male	brain
6	chr1:45480800-45510400	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:45481200-45504600	Weak transcription	Colonic Mucosa	Colon
8	chr1:45481200-45510200	Weak transcription	Lung	lung
9	chr1:45481200-45525000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:45481200-45527400	Weak transcription	Left Ventricle	heart
11	chr1:45481400-45500000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:45481600-45491800	Weak transcription	NHDF-Ad	bronchial
13	chr1:45481600-45498600	Weak transcription	Hela-S3	cervix
14	chr1:45481600-45499800	Weak transcription	Fetal Intestine Large	intestine
15	chr1:45481600-45499800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:45481800-45491400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:45481800-45499800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:45482000-45490600	Weak transcription	Fetal Lung	lung
19	chr1:45482000-45523800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:45484200-45499800	Weak transcription	Fetal Stomach	stomach
21	chr1:45484400-45499200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:45484600-45494800	Weak transcription	Right Atrium	heart
23	chr1:45484600-45499800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:45484800-45497800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:45484800-45499200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:45484800-45499400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:45484800-45499800	Weak transcription	Brain Angular Gyrus	brain
28	chr1:45484800-45499800	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:45485000-45499800	Weak transcription	Brain Substantia Nigra	brain
30	chr1:45485800-45501400	Weak transcription	Ovary	ovary
31	chr1:45486400-45496600	Weak transcription	Fetal Intestine Small	intestine
32	chr1:45486600-45499200	Weak transcription	Brain Anterior Caudate	brain
33	chr1:45487400-45498600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:45487400-45499200	Weak transcription	Brain Germinal Matrix	brain
35	chr1:45489800-45491400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:45489800-45499800	Weak transcription	Fetal Brain Female	brain

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