Variant report

Variant	rs12143560
Chromosome Location	chr1:45502875-45502876
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	chr1:45185795..45187646-chr1:45502768..45506079,3	K562	blood:
2	chr1:45500321..45502356-chr1:45502649..45504845,2	K562	blood:

Variant related genes	Relation type
ENSG00000199377	Chromatin interaction

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

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

rs_ID	r²[population]
rs10465876	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10749854	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11211066	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11211067	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11801218	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11809982	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12118189	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12134146	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12142302	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12239165	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12724597	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12731245	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12735549	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12739545	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12749939	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12755751	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12760109	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13948	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2050869	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236576	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2275598	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2275599	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2298005	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3806405	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6678726	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7514998	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7521339	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7525733	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7535347	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7541207	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7541351	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8681	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs998418	0.92[AMR][1000 genomes];0.92[EUR][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	nsv546148	chr1:45500294-45627663	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12143560	UROD	cis	Thyroid	GTEx
rs12143560	UROD	cis	Artery Tibial	GTEx
rs12143560	UROD	cis	Esophagus Muscularis	GTEx
rs12143560	UROD	cis	Nerve Tibial	GTEx
rs12143560	UROD	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45480800-45510400	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:45481200-45504600	Weak transcription	Colonic Mucosa	Colon
3	chr1:45481200-45510200	Weak transcription	Lung	lung
4	chr1:45481200-45525000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:45481200-45527400	Weak transcription	Left Ventricle	heart
6	chr1:45482000-45523800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:45491800-45516400	Weak transcription	Spleen	Spleen
8	chr1:45492000-45507600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:45494600-45504200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:45495000-45506800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:45497400-45525400	Weak transcription	Gastric	stomach
12	chr1:45498000-45525600	Weak transcription	Pancreas	Pancrea
13	chr1:45498200-45506800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:45499200-45516200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:45499600-45503200	Weak transcription	GM12878-XiMat	blood
16	chr1:45500000-45504800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:45500400-45505200	Weak transcription	Right Ventricle	heart
18	chr1:45500400-45516600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:45501400-45516600	Weak transcription	Small Intestine	intestine
20	chr1:45501600-45504800	Enhancers	Fetal Intestine Large	intestine
21	chr1:45501800-45504400	Enhancers	K562	blood
22	chr1:45501800-45505800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:45501800-45508000	Weak transcription	Brain Substantia Nigra	brain
24	chr1:45501800-45516200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:45501800-45521200	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:45501800-45527000	Weak transcription	Fetal Brain Male	brain
27	chr1:45502000-45503200	Weak transcription	Brain Anterior Caudate	brain
28	chr1:45502000-45503600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:45502000-45503800	Weak transcription	Ovary	ovary
30	chr1:45502000-45504000	Weak transcription	Brain Germinal Matrix	brain
31	chr1:45502000-45504000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:45502000-45504000	Weak transcription	HepG2	liver
33	chr1:45502000-45507600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:45502000-45507600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:45502000-45508000	Weak transcription	Brain Angular Gyrus	brain
36	chr1:45502000-45508000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:45502000-45508000	Weak transcription	Fetal Brain Female	brain
38	chr1:45502000-45508200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:45502000-45508600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:45502000-45510600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:45502000-45512800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:45502000-45523800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:45502400-45504000	Enhancers	Hela-S3	cervix
44	chr1:45502400-45505200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr1:45502400-45507800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:45502400-45523000	Weak transcription	Aorta	Aorta
47	chr1:45502600-45504200	Weak transcription	Fetal Stomach	stomach
48	chr1:45502800-45504200	Enhancers	Fetal Intestine Small	intestine

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