Variant report

Variant	rs7535347
Chromosome Location	chr1:45466511-45466512
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 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	chr1:45284681..45289780-chr1:45466475..45469909,5	MCF-7	breast:
4	chr1:45281186..45291350-chr1:45463934..45483092,44	K562	blood:
5	chr1:45464897..45467807-chr1:46048643..46051283,4	K562	blood:
6	chr1:45466176..45467776-chr1:45467983..45470171,2	MCF-7	breast:
7	chr1:45450854..45457330-chr1:45465047..45472849,14	K562	blood:
8	chr1:45258952..45260849-chr1:45465146..45466652,2	MCF-7	breast:

No data

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

Extended variants
information (count: 96 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10465876	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10749854	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10890316	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10890317	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10890318	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11211060	0.81[EUR][1000 genomes]
rs11211066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211067	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11556200	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11576875	0.81[EUR][1000 genomes]
rs11801218	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11802780	0.81[EUR][1000 genomes]
rs11806079	0.81[EUR][1000 genomes]
rs11809982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12070692	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12118189	0.90[EUR][1000 genomes]
rs12125188	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12125367	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap]
rs12126314	0.84[CEU][hapmap];0.84[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12126318	0.84[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.82[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12127012	0.81[EUR][1000 genomes]
rs12133015	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12134146	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12139143	0.85[CHD][hapmap]
rs12142302	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12142881	0.81[AMR][1000 genomes]
rs12143560	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12239165	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1226360	0.84[AMR][1000 genomes]
rs1226361	0.84[AMR][1000 genomes]
rs12724597	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12724852	0.81[EUR][1000 genomes]
rs12731245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12732402	0.81[EUR][1000 genomes]
rs12735549	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12735637	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap]
rs12738406	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12738542	0.83[CEU][hapmap];0.83[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12739545	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12749130	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.81[EUR][1000 genomes]
rs12749939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12750107	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12755554	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs12755751	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12758547	0.81[EUR][1000 genomes]
rs12760109	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17393404	0.81[EUR][1000 genomes]
rs183809	0.84[CEU][hapmap]
rs2050869	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2236576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2275598	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2275599	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2298005	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs263988	0.82[AMR][1000 genomes]
rs263989	0.84[CEU][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs263991	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs263992	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs263994	0.82[AMR][1000 genomes]
rs263996	0.82[AMR][1000 genomes]
rs263997	0.82[AMR][1000 genomes]
rs264020	0.84[AMR][1000 genomes]
rs264021	0.83[AMR][1000 genomes]
rs264022	0.84[CEU][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs264025	0.84[CEU][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs28409260	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs364482	0.89[CHD][hapmap];0.91[MEX][hapmap]
rs3806405	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4399199	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.82[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs544144	0.82[AMR][1000 genomes]
rs566063	0.84[AMR][1000 genomes]
rs56875328	0.81[EUR][1000 genomes]
rs656780	0.84[AMR][1000 genomes]
rs6659033	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6659777	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6666806	0.90[GIH][hapmap]
rs6671633	0.82[GIH][hapmap]
rs6678726	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6678762	0.81[EUR][1000 genomes]
rs6678769	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6692713	0.84[CEU][hapmap];0.84[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6703452	0.85[CHD][hapmap]
rs67863058	0.82[AMR][1000 genomes]
rs7514998	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7517439	0.85[CHD][hapmap]
rs7521339	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7541207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7541351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7553658	0.84[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8681	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998418	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7535347	UROD	cis	Adipose Subcutaneous	GTEx
rs7535347	EIF2B3	cis	parietal	SCAN
rs7535347	SNORD55	cis	parietal	SCAN
rs7535347	UROD	cis	Nerve Tibial	GTEx
rs7535347	EIF2B3	cis	cerebellum	SCAN
rs7535347	UROD	cis	Esophagus Muscularis	GTEx
rs7535347	UROD	cis	Artery Tibial	GTEx
rs7535347	TMEM69	cis	cerebellum	SCAN
rs7535347	UROD	cis	multi-tissue	Pritchard
rs7535347	SNORD55	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45452800-45466600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:45452800-45467800	Weak transcription	Osteobl	bone
3	chr1:45452800-45475200	Weak transcription	Right Atrium	heart
4	chr1:45454600-45467800	Weak transcription	K562	blood
5	chr1:45459800-45468400	Weak transcription	Fetal Lung	lung
6	chr1:45460200-45467600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:45460600-45467000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:45460800-45468400	Weak transcription	HepG2	liver
9	chr1:45463400-45466600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:45463800-45466800	Weak transcription	Fetal Stomach	stomach
11	chr1:45464000-45466800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:45464200-45466600	Weak transcription	Fetal Brain Female	brain
13	chr1:45464400-45466800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:45464400-45466800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:45464400-45467200	Weak transcription	Brain Germinal Matrix	brain
16	chr1:45464400-45467400	Weak transcription	Esophagus	oesophagus
17	chr1:45464400-45467600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:45464600-45466800	Weak transcription	Primary T cells from cord blood	blood
19	chr1:45464600-45467000	Weak transcription	Colonic Mucosa	Colon
20	chr1:45464600-45468000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:45464800-45467000	Weak transcription	NHLF	lung
22	chr1:45464800-45467400	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:45464800-45467600	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:45464800-45467600	Weak transcription	Ovary	ovary
25	chr1:45464800-45467800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:45464800-45468600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:45465000-45467400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:45465000-45467600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:45465000-45467600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:45465000-45467600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:45465000-45467600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:45465000-45470200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:45465200-45467000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:45465200-45467400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:45465200-45467600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:45465200-45467800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr1:45465400-45466600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:45465400-45467400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:45465400-45467600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:45465400-45467600	Weak transcription	Brain Angular Gyrus	brain
41	chr1:45465400-45467600	Weak transcription	Brain Anterior Caudate	brain
42	chr1:45465400-45467600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:45465400-45467600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:45465400-45467600	Weak transcription	Thymus	Thymus
45	chr1:45465400-45467800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr1:45465400-45467800	Weak transcription	NH-A	brain
47	chr1:45465400-45468000	Enhancers	Adipose Nuclei	Adipose
48	chr1:45465600-45467400	Weak transcription	Fetal Thymus	thymus
49	chr1:45465600-45467600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:45465600-45467600	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links