Variant report

Variant	rs2275599
Chromosome Location	chr1:45474750-45474751
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45469387..45472063-chr1:45473604..45475987,2	MCF-7	breast:
2	chr1:45474418..45476530-chr1:46048462..46051158,2	K562	blood:
3	chr1:45451325..45453836-chr1:45473269..45474967,2	MCF-7	breast:
4	chr1:45282320..45290015-chr1:45470338..45482903,45	K562	blood:
5	chr1:45194719..45198675-chr1:45474706..45481379,10	K562	blood:
6	chr1:45281186..45291350-chr1:45463934..45483092,44	K562	blood:
7	chr1:45469532..45472999-chr1:45473175..45475841,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126107	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000070785	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000202444	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10465876	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10749854	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10890316	0.85[AMR][1000 genomes]
rs10890317	0.83[AMR][1000 genomes]
rs10890318	0.83[AMR][1000 genomes]
rs11211066	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211067	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11556200	0.82[AFR][1000 genomes]
rs11801218	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11809982	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12070692	0.82[AFR][1000 genomes]
rs12118189	0.92[EUR][1000 genomes]
rs12125188	0.81[AFR][1000 genomes]
rs12126314	0.83[AMR][1000 genomes]
rs12126318	0.83[AMR][1000 genomes]
rs12133015	0.81[AMR][1000 genomes]
rs12134146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142302	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12143560	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12239165	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1226360	0.83[AMR][1000 genomes]
rs1226361	0.83[AMR][1000 genomes]
rs12724597	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12731245	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12735549	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12738406	0.83[AMR][1000 genomes]
rs12738542	0.83[AMR][1000 genomes]
rs12739545	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749939	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12750107	0.83[AMR][1000 genomes]
rs12755751	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12760109	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13948	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2050869	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2236576	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2275598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298005	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263988	0.81[AMR][1000 genomes]
rs263989	0.81[AMR][1000 genomes]
rs263991	0.81[AMR][1000 genomes]
rs263992	0.81[AMR][1000 genomes]
rs263994	0.81[AMR][1000 genomes]
rs263996	0.81[AMR][1000 genomes]
rs263997	0.81[AMR][1000 genomes]
rs264020	0.83[AMR][1000 genomes]
rs264021	0.82[AMR][1000 genomes]
rs264022	0.81[AMR][1000 genomes]
rs264025	0.81[AMR][1000 genomes]
rs28409260	0.81[AFR][1000 genomes]
rs3806405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4399199	0.83[AMR][1000 genomes]
rs544144	0.81[AMR][1000 genomes]
rs566063	0.83[AMR][1000 genomes]
rs656780	0.83[AMR][1000 genomes]
rs6659033	0.83[AMR][1000 genomes]
rs6659777	0.83[AMR][1000 genomes]
rs6678726	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6678769	0.81[AFR][1000 genomes]
rs6692713	0.83[AMR][1000 genomes]
rs67863058	0.81[AMR][1000 genomes]
rs7514998	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7521339	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7525733	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7535347	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7541207	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541351	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7553658	0.84[AMR][1000 genomes]
rs8681	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs998418	0.96[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2275599	UROD	cis	Nerve Tibial	GTEx
rs2275599	UROD	cis	Esophagus Muscularis	GTEx
rs2275599	UROD	cis	Artery Tibial	GTEx
rs2275599	UROD	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45452800-45475200	Weak transcription	Right Atrium	heart
2	chr1:45466600-45474800	Strong transcription	Fetal Brain Female	brain
3	chr1:45466600-45475000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:45466800-45475000	Strong transcription	Duodenum Mucosa	Duodenum
5	chr1:45466800-45475200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:45466800-45475200	Strong transcription	Primary T cells from cord blood	blood
7	chr1:45466800-45475200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:45466800-45475200	Strong transcription	Fetal Stomach	stomach
9	chr1:45467000-45474800	Strong transcription	Colonic Mucosa	Colon
10	chr1:45467000-45475200	Strong transcription	NHLF	lung
11	chr1:45467000-45475400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:45467000-45475400	Weak transcription	Psoas Muscle	Psoas
13	chr1:45467000-45476400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:45467200-45475200	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:45467400-45474800	Strong transcription	Fetal Muscle Leg	muscle
16	chr1:45467400-45474800	Strong transcription	Spleen	Spleen
17	chr1:45467400-45475000	Strong transcription	Esophagus	oesophagus
18	chr1:45467400-45475200	Strong transcription	Lung	lung
19	chr1:45467400-45475200	Strong transcription	Placenta Amnion	Placenta Amnion
20	chr1:45467400-45475400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:45467400-45475400	Strong transcription	Fetal Thymus	thymus
22	chr1:45467400-45475400	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:45467600-45474800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:45467600-45474800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:45467600-45474800	Strong transcription	Brain Angular Gyrus	brain
26	chr1:45467600-45474800	Strong transcription	Placenta	Placenta
27	chr1:45467600-45474800	Strong transcription	Ovary	ovary
28	chr1:45467600-45475000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:45467600-45475000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:45467600-45475000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:45467600-45475000	Strong transcription	Brain Anterior Caudate	brain
32	chr1:45467600-45475200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:45467600-45475200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr1:45467600-45475200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:45467600-45475200	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:45467600-45475200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:45467600-45475200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:45467600-45475200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:45467600-45475200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:45467600-45475200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr1:45467600-45475400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:45467600-45475400	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:45467600-45475400	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr1:45467600-45475400	Strong transcription	Thymus	Thymus
45	chr1:45467600-45475600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:45467800-45474800	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:45467800-45474800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:45467800-45475000	Strong transcription	Primary hematopoietic stem cells	blood
49	chr1:45467800-45475000	Strong transcription	Brain Hippocampus Middle	brain
50	chr1:45467800-45475000	Strong transcription	Brain Inferior Temporal Lobe	brain

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