Variant report

Variant	rs12139143
Chromosome Location	chr1:45350028-45350029
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45348967..45351344-chr1:45356459..45358965,2	K562	blood:
2	chr1:45307028..45308891-chr1:45347819..45350081,2	K562	blood:
3	chr1:45344734..45347015-chr1:45348415..45350873,2	K562	blood:
4	chr1:45284000..45285938-chr1:45349636..45351440,2	K562	blood:
5	chr1:45257422..45260349-chr1:45347384..45350306,2	K562	blood:

Variant related genes	Relation type
ENSG00000117425	Chromatin interaction
ENSG00000202444	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10890313	0.93[CEU][hapmap]
rs11211025	0.92[CEU][hapmap]
rs11211026	0.93[CEU][hapmap]
rs11211036	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11211038	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.86[ASN][1000 genomes]
rs11211040	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211045	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211048	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211051	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211053	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11211066	0.85[CHD][hapmap]
rs1140279	0.93[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.80[ASN][1000 genomes]
rs11556200	0.84[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap]
rs11573542	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11573557	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11573559	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11573562	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11573592	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11584440	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.89[ASN][1000 genomes]
rs11801990	0.89[CHB][hapmap]
rs11803622	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.81[TSI][hapmap]
rs11806832	0.90[ASN][1000 genomes]
rs11809931	0.83[ASN][1000 genomes]
rs12125367	0.84[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap]
rs12126314	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs12126318	0.84[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap]
rs12126557	0.84[CEU][hapmap]
rs12144152	0.81[ASN][1000 genomes]
rs12569156	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12723764	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12729917	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12732939	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs12733586	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12735038	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12735637	0.84[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap]
rs12738360	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12738542	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs12741443	0.81[ASN][1000 genomes]
rs12746270	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.80[ASN][1000 genomes]
rs12749130	0.84[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap]
rs12755554	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs13948	0.85[CHD][hapmap]
rs16832227	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs16832263	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16832265	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17881698	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.89[ASN][1000 genomes]
rs17883049	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.89[ASN][1000 genomes]
rs17886118	0.89[ASN][1000 genomes]
rs183809	0.84[CHB][hapmap]
rs2236576	0.85[CHD][hapmap]
rs2295997	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2295998	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2295999	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs263989	0.84[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap]
rs263991	0.84[CHB][hapmap]
rs263992	0.83[CHB][hapmap]
rs264022	0.84[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap]
rs264025	0.84[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap]
rs34436945	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34506400	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34541568	0.82[ASN][1000 genomes]
rs34639510	0.87[ASN][1000 genomes]
rs34984079	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35343809	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35957134	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs364482	0.84[CHB][hapmap];0.96[CHD][hapmap]
rs3795713	0.80[ASN][1000 genomes]
rs3795714	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs3795719	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3806405	0.85[CHD][hapmap]
rs3820586	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap]
rs4342887	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.80[ASN][1000 genomes]
rs4399199	0.84[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap]
rs6429549	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6429550	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6676749	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.87[ASN][1000 genomes]
rs6678726	0.82[CHD][hapmap]
rs6689911	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.80[ASN][1000 genomes]
rs6692487	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6692713	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs6697153	0.83[ASN][1000 genomes]
rs6703452	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67408784	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7517439	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7517639	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7525733	0.85[CHD][hapmap]
rs7527787	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7528461	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7531019	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7534487	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs7535347	0.85[CHD][hapmap]
rs7536078	0.89[CHB][hapmap]
rs7541207	0.85[CHD][hapmap]
rs7546285	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs7553658	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs8681	0.85[CHD][hapmap]
rs998418	0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12139143	UROD	cis	Esophagus Muscularis	GTEx
rs12139143	ZNF691	cis	cerebellum	SCAN
rs12139143	UROD	cis	Artery Tibial	GTEx
rs12139143	TIE1	cis	parietal	SCAN
rs12139143	SNORD55	cis	parietal	SCAN
rs12139143	EIF2B3	cis	cerebellum	SCAN
rs12139143	UROD	cis	lung	GTEx
rs12139143	UROD	cis	Adipose Subcutaneous	GTEx
rs12139143	SNORD55	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45309200-45360600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:45309400-45350400	Weak transcription	HUVEC	blood vessel
3	chr1:45309600-45352400	Weak transcription	Fetal Heart	heart
4	chr1:45309600-45354200	Weak transcription	Fetal Brain Male	brain
5	chr1:45313400-45360200	Weak transcription	Hela-S3	cervix
6	chr1:45316600-45351800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:45317800-45355600	Weak transcription	NHDF-Ad	bronchial
8	chr1:45322000-45350400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:45322600-45360000	Weak transcription	Small Intestine	intestine
10	chr1:45326800-45350400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:45331200-45352200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:45331600-45352400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:45332600-45357200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:45333400-45357000	Weak transcription	Fetal Kidney	kidney
15	chr1:45334600-45371800	Weak transcription	Gastric	stomach
16	chr1:45337400-45355600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:45340800-45361800	Weak transcription	Aorta	Aorta
18	chr1:45341200-45352200	Weak transcription	Fetal Lung	lung
19	chr1:45341200-45354000	Weak transcription	Stomach Mucosa	stomach
20	chr1:45341200-45355600	Weak transcription	NHLF	lung
21	chr1:45341400-45354800	Weak transcription	Psoas Muscle	Psoas
22	chr1:45344000-45352200	Weak transcription	HepG2	liver
23	chr1:45345400-45350200	Weak transcription	Brain Substantia Nigra	brain
24	chr1:45345600-45350400	Weak transcription	Ovary	ovary
25	chr1:45345600-45350800	Strong transcription	K562	blood
26	chr1:45345600-45366200	Weak transcription	Esophagus	oesophagus
27	chr1:45345800-45350400	Weak transcription	Left Ventricle	heart
28	chr1:45345800-45350600	Weak transcription	Placenta	Placenta
29	chr1:45345800-45363600	Weak transcription	Colonic Mucosa	Colon
30	chr1:45346000-45350600	Weak transcription	Brain Germinal Matrix	brain
31	chr1:45346000-45352400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:45346200-45353800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:45346200-45359200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:45346400-45363200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr1:45347400-45350200	Weak transcription	Brain Angular Gyrus	brain
36	chr1:45347400-45350400	Weak transcription	Pancreas	Pancrea
37	chr1:45347400-45352200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:45347600-45350400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:45347600-45350400	Weak transcription	Fetal Brain Female	brain
40	chr1:45347600-45350400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr1:45347600-45350600	Weak transcription	Spleen	Spleen
42	chr1:45347600-45352200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:45347600-45353400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:45347600-45353800	Weak transcription	HSMMtube	muscle
45	chr1:45347600-45353800	Weak transcription	Osteobl	bone
46	chr1:45347600-45354400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:45347600-45356400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr1:45347600-45358800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:45347600-45360400	Weak transcription	HMEC	breast
50	chr1:45347600-45362600	Weak transcription	Lung	lung

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