Variant report

Variant	rs263998
Chromosome Location	chr1:45438877-45438878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45436208..45437832-chr1:45438280..45440463,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11211046	0.82[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap]
rs11573543	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs12059964	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs1226572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263965	0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs263966	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs263975	0.86[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs263977	0.81[ASN][1000 genomes]
rs263980	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs263982	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs263987	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263990	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs264005	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs264009	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs264011	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs264014	1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3121173	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36107413	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3795720	0.97[CHD][hapmap]
rs398200	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399628	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs401665	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs438493	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs452989	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs489676	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61789958	0.86[ASN][1000 genomes]
rs620764	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6429548	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs659293	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6666806	0.80[CHD][hapmap]
rs6671633	0.80[ASW][hapmap];0.82[YRI][hapmap]
rs746320	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7526786	0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap]
rs7554177	0.97[CHD][hapmap]
rs9429058	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9988451	0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap]

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	esv2830314	chr1:45430218-45455285	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs263998	UROD	cis	multi-tissue	Pritchard
rs263998	EIF2B3	cis	cerebellum	SCAN
rs263998	EIF2B3	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45389200-45450200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:45391200-45439800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:45392800-45443200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:45412000-45440000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:45412800-45441000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:45413400-45439600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:45413400-45439800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:45413400-45441400	Weak transcription	Brain Anterior Caudate	brain
9	chr1:45413600-45441400	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:45413600-45442800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:45413800-45439800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:45413800-45441600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:45414000-45439400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:45414000-45439600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:45414000-45440000	Weak transcription	Brain Angular Gyrus	brain
16	chr1:45414000-45440000	Weak transcription	Fetal Lung	lung
17	chr1:45414000-45441000	Weak transcription	Fetal Kidney	kidney
18	chr1:45414000-45441600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:45414000-45443200	Weak transcription	Pancreas	Pancrea
20	chr1:45414000-45450800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:45414000-45451000	Weak transcription	Spleen	Spleen
22	chr1:45414200-45443000	Weak transcription	Gastric	stomach
23	chr1:45415600-45440400	Weak transcription	Fetal Brain Female	brain
24	chr1:45416600-45443600	Weak transcription	Psoas Muscle	Psoas
25	chr1:45417600-45442000	Weak transcription	Placenta	Placenta
26	chr1:45421000-45450800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:45421400-45443400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr1:45422000-45441400	Weak transcription	Esophagus	oesophagus
29	chr1:45423400-45439600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:45423600-45441400	Weak transcription	NHLF	lung
31	chr1:45424200-45440800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:45424600-45439000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:45424600-45439400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:45424600-45441400	Weak transcription	Lung	lung
35	chr1:45424600-45443200	Weak transcription	Thymus	Thymus
36	chr1:45424800-45439800	Weak transcription	Left Ventricle	heart
37	chr1:45424800-45440600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr1:45424800-45445600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:45425000-45439800	Weak transcription	Fetal Intestine Large	intestine
40	chr1:45425000-45445600	Weak transcription	Aorta	Aorta
41	chr1:45425200-45439800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:45425600-45443400	Weak transcription	HSMMtube	muscle
43	chr1:45429200-45440800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:45430600-45441600	Weak transcription	HepG2	liver
45	chr1:45430800-45440800	Weak transcription	NHEK	skin
46	chr1:45430800-45450800	Weak transcription	Brain Substantia Nigra	brain
47	chr1:45432200-45443800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:45432400-45442200	Weak transcription	Brain Germinal Matrix	brain
49	chr1:45432600-45440800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:45432600-45440800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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