Variant report

Variant	rs263990
Chromosome Location	chr1:45441317-45441318
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45284052..45287183-chr1:45440779..45443928,3	K562	blood:
2	chr1:45441142..45443966-chr1:45451667..45454449,3	K562	blood:
3	chr1:45430590..45432812-chr1:45438899..45441605,3	K562	blood:
4	chr1:45430590..45432812-chr1:45438899..45441605,2	K562	blood:

Variant related genes	Relation type
ENSG00000202444	Chromatin interaction
ENSG00000232369	Chromatin interaction
ENSG00000070785	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

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];0.89[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];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263965	0.86[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs263966	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs263975	0.86[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.81[ASN][1000 genomes]
rs263977	0.81[ASN][1000 genomes]
rs263980	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs263982	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs263987	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263998	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs264005	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs264009	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[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];0.95[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs264014	1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3121173	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36107413	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3795720	0.97[CHD][hapmap]
rs398200	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399628	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs401665	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs438493	0.86[AMR][1000 genomes];0.91[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];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs489676	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61789958	0.86[ASN][1000 genomes]
rs620764	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6429548	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs659293	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[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];0.89[YRI][hapmap]
rs7554177	0.97[CHD][hapmap]
rs9429058	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9988451	0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.89[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs263990	EIF2B3	cis	parietal	SCAN
rs263990	UROD	cis	multi-tissue	Pritchard
rs263990	EIF2B3	cis	cerebellum	SCAN
rs263990	UROD	cis	Esophagus Muscularis	GTEx

Chromatin state (count:122 , 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	chr1:45392800-45443200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:45413400-45441400	Weak transcription	Brain Anterior Caudate	brain
4	chr1:45413600-45441400	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:45413600-45442800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:45413800-45441600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:45414000-45441600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:45414000-45443200	Weak transcription	Pancreas	Pancrea
9	chr1:45414000-45450800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:45414000-45451000	Weak transcription	Spleen	Spleen
11	chr1:45414200-45443000	Weak transcription	Gastric	stomach
12	chr1:45416600-45443600	Weak transcription	Psoas Muscle	Psoas
13	chr1:45417600-45442000	Weak transcription	Placenta	Placenta
14	chr1:45421000-45450800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:45421400-45443400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:45422000-45441400	Weak transcription	Esophagus	oesophagus
17	chr1:45423600-45441400	Weak transcription	NHLF	lung
18	chr1:45424600-45441400	Weak transcription	Lung	lung
19	chr1:45424600-45443200	Weak transcription	Thymus	Thymus
20	chr1:45424800-45445600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:45425000-45445600	Weak transcription	Aorta	Aorta
22	chr1:45425600-45443400	Weak transcription	HSMMtube	muscle
23	chr1:45430600-45441600	Weak transcription	HepG2	liver
24	chr1:45430800-45450800	Weak transcription	Brain Substantia Nigra	brain
25	chr1:45432200-45443800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:45432400-45442200	Weak transcription	Brain Germinal Matrix	brain
27	chr1:45432600-45442000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:45433200-45451000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:45433400-45443000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:45434400-45450800	Weak transcription	Small Intestine	intestine
31	chr1:45435600-45444200	Strong transcription	Primary T cells from cord blood	blood
32	chr1:45435600-45447400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:45435600-45447600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:45436000-45447000	Strong transcription	Fetal Muscle Leg	muscle
35	chr1:45436200-45446800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:45436400-45450800	Weak transcription	HMEC	breast
37	chr1:45436600-45450800	Weak transcription	Stomach Mucosa	stomach
38	chr1:45436800-45442000	Weak transcription	NH-A	brain
39	chr1:45436800-45445000	Weak transcription	Hela-S3	cervix
40	chr1:45437200-45444200	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:45437200-45446800	Strong transcription	Fetal Thymus	thymus
42	chr1:45437400-45442000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:45437400-45444800	Weak transcription	HUVEC	blood vessel
44	chr1:45437400-45446600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:45437400-45447400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr1:45437600-45441600	Strong transcription	Fetal Stomach	stomach
47	chr1:45437600-45446800	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:45437600-45447000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:45437600-45447200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr1:45437800-45441800	Strong transcription	Adipose Nuclei	Adipose

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