Variant report

Variant	rs6666806
Chromosome Location	chr1:45466927-45466928
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45465440..45468490-chr1:45474969..45479261,5	MCF-7	breast:
2	chr1:45465674..45468338-chr1:45474492..45477550,3	MCF-7	breast:
3	chr1:45284388..45285918-chr1:45466927..45469619,2	MCF-7	breast:
4	chr1:45284681..45289780-chr1:45466475..45469909,5	MCF-7	breast:
5	chr1:45281186..45291350-chr1:45463934..45483092,44	K562	blood:
6	chr1:45464897..45467807-chr1:46048643..46051283,4	K562	blood:
7	chr1:45450275..45452843-chr1:45466530..45468587,2	MCF-7	breast:
8	chr1:45466176..45467776-chr1:45467983..45470171,2	MCF-7	breast:
9	chr1:45450854..45457330-chr1:45465047..45472849,14	K562	blood:

No data

Variant related genes	Relation type
ENSG00000132780	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000070785	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000232369	Chromatin interaction
ENSG00000126107	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10890319	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211066	0.90[GIH][hapmap]
rs11211067	0.86[YRI][hapmap]
rs12047556	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12094272	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13948	0.90[GIH][hapmap]
rs1964030	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2236576	0.90[GIH][hapmap]
rs2298006	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263966	0.80[CHD][hapmap]
rs263990	0.80[CHD][hapmap]
rs264011	0.80[CHD][hapmap]
rs3806405	0.90[GIH][hapmap]
rs452989	0.80[CHD][hapmap]
rs4660290	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660830	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6671633	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6678726	0.87[GIH][hapmap]
rs7521006	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7525733	0.90[GIH][hapmap]
rs7535347	0.90[GIH][hapmap]
rs7537361	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7541207	0.90[GIH][hapmap]
rs7551698	0.89[YRI][hapmap]
rs8681	0.90[GIH][hapmap]
rs998418	0.87[GIH][hapmap];0.90[YRI][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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6666806	UROD	cis	multi-tissue	Pritchard
rs6666806	EIF2B3	cis	parietal	SCAN
rs6666806	UROD	cis	Adipose Subcutaneous	GTEx
rs6666806	UROD	cis	Artery Tibial	GTEx
rs6666806	EIF2B3	cis	cerebellum	SCAN
rs6666806	SNORD55	cis	cerebellum	SCAN
rs6666806	SNORD55	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45452800-45467800	Weak transcription	Osteobl	bone
2	chr1:45452800-45475200	Weak transcription	Right Atrium	heart
3	chr1:45454600-45467800	Weak transcription	K562	blood
4	chr1:45459800-45468400	Weak transcription	Fetal Lung	lung
5	chr1:45460200-45467600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:45460600-45467000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:45460800-45468400	Weak transcription	HepG2	liver
8	chr1:45464400-45467200	Weak transcription	Brain Germinal Matrix	brain
9	chr1:45464400-45467400	Weak transcription	Esophagus	oesophagus
10	chr1:45464400-45467600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr1:45464600-45467000	Weak transcription	Colonic Mucosa	Colon
12	chr1:45464600-45468000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:45464800-45467000	Weak transcription	NHLF	lung
14	chr1:45464800-45467400	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:45464800-45467600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:45464800-45467600	Weak transcription	Ovary	ovary
17	chr1:45464800-45467800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:45464800-45468600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:45465000-45467400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:45465000-45467600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:45465000-45467600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:45465000-45467600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:45465000-45467600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:45465000-45470200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:45465200-45467000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:45465200-45467400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:45465200-45467600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:45465200-45467800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:45465400-45467400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:45465400-45467600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:45465400-45467600	Weak transcription	Brain Angular Gyrus	brain
32	chr1:45465400-45467600	Weak transcription	Brain Anterior Caudate	brain
33	chr1:45465400-45467600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:45465400-45467600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:45465400-45467600	Weak transcription	Thymus	Thymus
36	chr1:45465400-45467800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:45465400-45467800	Weak transcription	NH-A	brain
38	chr1:45465400-45468000	Enhancers	Adipose Nuclei	Adipose
39	chr1:45465600-45467400	Weak transcription	Fetal Thymus	thymus
40	chr1:45465600-45467600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:45465600-45467600	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr1:45465600-45467600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:45465600-45467600	Weak transcription	NHEK	skin
44	chr1:45465600-45467800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr1:45465600-45467800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:45465600-45467800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:45465600-45467800	Weak transcription	HSMM	muscle
48	chr1:45465800-45467600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:45465800-45467600	Weak transcription	Placenta	Placenta
50	chr1:45465800-45467800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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