Variant report

Variant	rs2298005
Chromosome Location	chr1:45476663-45476664
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:84)
CpG islands
(count:0)
Chromatin interactive
region (count:30)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:84 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:45476660-45476810	HMEC	breast:	n/a	n/a
2	MAX	chr1:45476650-45477303	A549	lung:	n/a	n/a
3	YY1	chr1:45476071-45477182	HepG2	liver:	n/a	chr1:45476417-45476428
4	MYC	chr1:45476508-45477273	K562	blood:	n/a	n/a
5	CTCF	chr1:45476660-45476810	HUVEC	blood vessel:	n/a	n/a
6	MAX	chr1:45476655-45477221	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:45476631-45477353	GM12878	blood:	n/a	n/a
8	MAFK	chr1:45476621-45478788	GM12878	blood:	n/a	chr1:45477404-45477414
9	CTBP2	chr1:45476090-45477121	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr1:45476484-45477270	ECC-1	luminal epithelium:	n/a	n/a
11	ETS1	chr1:45476484-45477198	K562	blood:	n/a	n/a
12	HA-E2F1	chr1:45476136-45477334	MCF-7	breast:	n/a	chr1:45476451-45476462
13	MAX	chr1:45476214-45477195	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:45476531-45477115	GM12878	blood:	n/a	n/a
15	SIN3AK20	chr1:45476445-45477210	K562	blood:	n/a	n/a
16	MAX	chr1:45476538-45477234	NB4	blood:	n/a	n/a
17	SIN3AK20	chr1:45475934-45478388	MCF-7	breast:	n/a	n/a
18	HCFC1	chr1:45476110-45478872	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:45476545-45477136	A549	lung:	n/a	n/a
20	CCNT2	chr1:45476219-45477167	K562	blood:	n/a	n/a
21	YY1	chr1:45476620-45477270	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr1:45476588-45477202	GM12878	blood:	n/a	n/a
23	MYC	chr1:45476554-45477210	NB4	blood:	n/a	n/a
24	UBTF	chr1:45476609-45476970	K562	blood:	n/a	n/a
25	NRF1	chr1:45476286-45476861	SK-N-SH	brain:	n/a	n/a
26	BACH1	chr1:45476548-45477184	H1-hESC	embryonic stem cell:	n/a	n/a
27	MXI1	chr1:45476325-45477218	HepG2	liver:	n/a	n/a
28	SMC3	chr1:45476129-45477249	Hela-S3	cervix:	n/a	n/a
29	PML	chr1:45476592-45478310	GM12878	blood:	n/a	chr1:45477407-45477416
30	YY1	chr1:45476456-45476758	GM12891	blood:	n/a	n/a
31	POLR2A	chr1:45476546-45477391	GM12892	blood:	n/a	n/a
32	MXI1	chr1:45476228-45477210	Hela-S3	cervix:	n/a	n/a
33	MAX	chr1:45476575-45477130	HepG2	liver:	n/a	n/a
34	MAZ	chr1:45476045-45478868	IMR90	lung:	n/a	chr1:45477970-45477980 chr1:45477973-45477980
35	ELF1	chr1:45476356-45477163	GM12878	blood:	n/a	n/a
36	TCF3	chr1:45476554-45477193	GM12878	blood:	n/a	n/a
37	MAX	chr1:45476467-45477181	K562	blood:	n/a	n/a
38	TCF12	chr1:45476131-45477276	ECC-1	luminal epithelium:	n/a	chr1:45476977-45476984
39	MXI1	chr1:45475602-45477470	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr1:45475934-45477219	MCF-7	breast:	n/a	n/a
41	CTCF	chr1:45476580-45476730	GM12872	blood:	n/a	n/a
42	POLR2A	chr1:45476625-45477262	SK-N-MC	brain:	n/a	n/a
43	MTA3	chr1:45476135-45478318	GM12878	blood:	n/a	n/a
44	HMGN3	chr1:45476158-45477455	K562	blood:	n/a	n/a
45	MAZ	chr1:45476488-45478947	K562	blood:	n/a	chr1:45477970-45477980 chr1:45477973-45477980
46	SIN3AK20	chr1:45475976-45477123	PANC-1	pancreas:	n/a	n/a
47	SIN3A	chr1:45476015-45478907	H1-hESC	embryonic stem cell:	n/a	chr1:45477790-45477799 chr1:45477793-45477806
48	YY1	chr1:45476269-45477286	GM12878	blood:	n/a	chr1:45476417-45476428
49	MXI1	chr1:45476309-45477255	GM12878	blood:	n/a	n/a
50	POLR2A	chr1:45476188-45477275	HUVEC	blood vessel:	n/a	n/a

No data

(count:30 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45305082..45310090-chr1:45475264..45482808,8	K562	blood:
2	chr1:45193444..45198675-chr1:45475617..45480324,16	K562	blood:
3	chr1:45269727..45273120-chr1:45475175..45479286,6	K562	blood:
4	chr1:45264279..45267905-chr1:45476139..45480748,9	K562	blood:
5	chr1:45239135..45244789-chr1:45475459..45482236,15	K562	blood:
6	chr1:45476252..45479466-chr1:46015891..46017851,3	K562	blood:
7	chr1:45471285..45474230-chr1:45476025..45477954,2	MCF-7	breast:
8	chr1:45476357..45485239-chr1:45761850..45773601,48	K562	blood:
9	chr1:45475180..45477058-chr1:45478388..45480349,2	MCF-7	breast:
10	chr1:45451300..45453679-chr1:45476530..45479236,3	MCF-7	breast:
11	chr1:45306981..45310503-chr1:45474976..45481200,7	K562	blood:
12	chr1:45449901..45454181-chr1:45475970..45480540,16	K562	blood:
13	chr1:45268954..45275189-chr1:45475024..45480055,7	K562	blood:
14	chr1:45282320..45290015-chr1:45470338..45482903,45	K562	blood:
15	chr1:45284268..45287037-chr1:45476110..45479807,4	MCF-7	breast:
16	chr1:45194719..45198675-chr1:45474706..45481379,10	K562	blood:
17	chr1:45184334..45189303-chr1:45475138..45480545,18	K562	blood:
18	chr1:45455788..45461421-chr1:45474837..45478788,5	MCF-7	breast:
19	chr1:45283389..45288095-chr1:45474959..45480313,6	MCF-7	breast:
20	chr1:45239617..45241510-chr1:45476171..45478089,2	MCF-7	breast:
21	chr1:45240714..45243157-chr1:45476342..45480108,4	MCF-7	breast:
22	chr1:45281186..45291350-chr1:45463934..45483092,44	K562	blood:
23	chr1:45194277..45197109-chr1:45476180..45479040,2	MCF-7	breast:
24	chr1:45476210..45477994-chr1:45804757..45807098,3	MCF-7	breast:
25	chr1:45273315..45275597-chr1:45475668..45479411,4	K562	blood:
26	chr1:45475963..45478525-chr1:45804448..45806898,2	MCF-7	breast:
27	chr1:45264355..45267553-chr1:45476139..45481796,8	K562	blood:
28	chr1:45184334..45189289-chr1:45475449..45480431,12	K562	blood:
29	chr1:45476265..45486633-chr1:45761064..45774272,63	K562	blood:
30	chr1:45470053..45471669-chr1:45475976..45477628,2	MCF-7	breast:

No data

Variant related genes	Relation type
UROD	TF binding region
HECTD3	TF binding region
ENSG00000222009	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000226499	Chromatin interaction
ENSG00000070785	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000268949	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000117425	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10465876	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10749854	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211059	0.82[AFR][1000 genomes]
rs11211066	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211067	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11576875	0.87[AFR][1000 genomes]
rs11801218	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11802780	0.85[AFR][1000 genomes]
rs11806079	0.85[AFR][1000 genomes]
rs11809982	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12117432	0.82[AFR][1000 genomes]
rs12118189	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12127012	0.87[AFR][1000 genomes]
rs12134146	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142302	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12143560	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12239165	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12724597	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12724852	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12731245	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12732402	0.87[AFR][1000 genomes]
rs12735549	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12739545	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12740561	0.82[AFR][1000 genomes]
rs12749130	0.85[AFR][1000 genomes]
rs12749939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12755751	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12758547	0.85[AFR][1000 genomes]
rs12760109	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13948	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17393404	0.85[AFR][1000 genomes]
rs2050869	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2236576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2275598	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275599	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806405	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56875328	0.87[AFR][1000 genomes]
rs6678726	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6678762	0.87[AFR][1000 genomes]
rs7514998	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7519454	0.82[AFR][1000 genomes]
rs7521339	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7525733	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7535347	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7541207	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541351	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8681	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs998418	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2298005	UROD	cis	Esophagus Muscularis	GTEx
rs2298005	UROD	cis	Nerve Tibial	GTEx
rs2298005	UROD	cis	Artery Tibial	GTEx
rs2298005	UROD	cis	Thyroid	GTEx
rs2298005	UROD	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45475400-45477600	Flanking Active TSS	Colonic Mucosa	Colon
2	chr1:45475600-45477000	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr1:45475600-45477000	Active TSS	HSMMtube	muscle
4	chr1:45475600-45477200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:45475600-45477200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:45475600-45477200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:45475600-45480400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:45475800-45477000	Active TSS	H9 Cell Line	embryonic stem cell
9	chr1:45475800-45477200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr1:45475800-45477200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr1:45475800-45478600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:45475800-45478800	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr1:45475800-45479200	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr1:45476000-45477000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:45476000-45477000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:45476000-45477000	Active TSS	Muscle Satellite Cultured Cells	--
17	chr1:45476000-45477000	Active TSS	Fetal Intestine Large	intestine
18	chr1:45476000-45477000	Active TSS	Fetal Kidney	kidney
19	chr1:45476000-45477000	Active TSS	HMEC	breast
20	chr1:45476000-45477000	Active TSS	NHDF-Ad	bronchial
21	chr1:45476000-45477000	Active TSS	NHEK	skin
22	chr1:45476000-45477200	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr1:45476000-45477200	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr1:45476000-45477200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:45476000-45477200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:45476000-45477200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:45476000-45477200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:45476000-45477200	Active TSS	Fetal Intestine Small	intestine
29	chr1:45476000-45477200	Active TSS	Right Atrium	heart
30	chr1:45476000-45477200	Active TSS	A549	lung
31	chr1:45476000-45477200	Active TSS	HSMM	muscle
32	chr1:45476000-45478600	Active TSS	Aorta	Aorta
33	chr1:45476000-45479000	Active TSS	Ovary	ovary
34	chr1:45476200-45476800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:45476200-45477000	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr1:45476200-45477000	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr1:45476200-45477000	Active TSS	Primary T cells from cord blood	blood
38	chr1:45476200-45477000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:45476200-45477000	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr1:45476200-45477000	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr1:45476200-45477000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:45476200-45477000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:45476200-45477000	Active TSS	Brain Angular Gyrus	brain
44	chr1:45476200-45477000	Active TSS	Brain Anterior Caudate	brain
45	chr1:45476200-45477000	Active TSS	Colon Smooth Muscle	Colon
46	chr1:45476200-45477000	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr1:45476200-45477000	Active TSS	Fetal Brain Female	brain
48	chr1:45476200-45477000	Active TSS	Fetal Lung	lung
49	chr1:45476200-45477000	Active TSS	Fetal Thymus	thymus
50	chr1:45476200-45477000	Active TSS	Gastric	stomach

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