Variant report

Variant	rs6671633
Chromosome Location	chr1:45500294-45500295
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45478386..45480410-chr1:45500265..45501883,2	K562	blood:
2	chr1:45498340..45501082-chr1:45804198..45806208,2	K562	blood:
3	chr1:45498340..45501082-chr1:45804198..45806724,3	K562	blood:

Variant related genes	Relation type
ENSG00000132773	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000132781	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10736425	0.82[AFR][1000 genomes]
rs10890319	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211066	0.82[GIH][hapmap]
rs11211067	0.83[YRI][hapmap]
rs11211072	0.95[AFR][1000 genomes]
rs12047556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094272	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226572	0.82[YRI][hapmap]
rs13948	0.82[GIH][hapmap]
rs1964030	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2236576	0.82[GIH][hapmap]
rs2298006	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263966	0.80[ASW][hapmap];0.82[YRI][hapmap]
rs263990	0.80[ASW][hapmap];0.82[YRI][hapmap]
rs264011	0.87[ASW][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs264014	0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs3806405	0.82[GIH][hapmap]
rs401665	0.80[AFR][1000 genomes]
rs452989	0.80[ASW][hapmap];0.82[YRI][hapmap]
rs4660290	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4660830	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489676	0.80[AFR][1000 genomes]
rs6666806	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	0.91[GIH][hapmap]
rs7521006	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525733	0.82[GIH][hapmap]
rs7535347	0.82[GIH][hapmap]
rs7537361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541207	0.82[GIH][hapmap]
rs7543818	0.95[AFR][1000 genomes]
rs7551698	0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs8681	0.82[GIH][hapmap]
rs998418	0.91[GIH][hapmap];0.80[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv546148	chr1:45500294-45627663	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6671633	UROD	cis	multi-tissue	Pritchard
rs6671633	EIF2B3	cis	cerebellum	SCAN
rs6671633	SNORD55	cis	cerebellum	SCAN
rs6671633	UROD	cis	Artery Tibial	GTEx
rs6671633	SNORD55	cis	parietal	SCAN
rs6671633	EIF2B3	cis	parietal	SCAN
rs6671633	UROD	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45480800-45500600	Weak transcription	HepG2	liver
2	chr1:45480800-45501200	Weak transcription	Fetal Brain Male	brain
3	chr1:45480800-45510400	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:45481200-45504600	Weak transcription	Colonic Mucosa	Colon
5	chr1:45481200-45510200	Weak transcription	Lung	lung
6	chr1:45481200-45525000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:45481200-45527400	Weak transcription	Left Ventricle	heart
8	chr1:45482000-45523800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:45485800-45501400	Weak transcription	Ovary	ovary
10	chr1:45491800-45516400	Weak transcription	Spleen	Spleen
11	chr1:45492000-45507600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:45494600-45504200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:45495000-45506800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:45497400-45525400	Weak transcription	Gastric	stomach
15	chr1:45497800-45501000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:45497800-45501800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:45498000-45525600	Weak transcription	Pancreas	Pancrea
18	chr1:45498200-45506800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:45498600-45502000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:45499200-45502000	Strong transcription	Brain Anterior Caudate	brain
21	chr1:45499200-45502000	Strong transcription	Brain Germinal Matrix	brain
22	chr1:45499200-45502000	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr1:45499200-45502400	Strong transcription	Stomach Smooth Muscle	stomach
24	chr1:45499200-45516200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:45499400-45500400	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:45499400-45501200	Strong transcription	Fetal Intestine Small	intestine
27	chr1:45499400-45501400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:45499400-45502000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:45499400-45502400	Weak transcription	Hela-S3	cervix
30	chr1:45499600-45503200	Weak transcription	GM12878-XiMat	blood
31	chr1:45499800-45501800	Strong transcription	Brain Hippocampus Middle	brain
32	chr1:45499800-45501800	Strong transcription	Brain Substantia Nigra	brain
33	chr1:45499800-45502000	Strong transcription	Brain Angular Gyrus	brain
34	chr1:45499800-45502000	Strong transcription	Brain Cingulate Gyrus	brain
35	chr1:45499800-45502000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:45499800-45502000	Strong transcription	Fetal Brain Female	brain
37	chr1:45499800-45502000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:45499800-45502600	Strong transcription	Fetal Stomach	stomach
39	chr1:45500000-45502000	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:45500000-45502000	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr1:45500000-45504800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr1:45500200-45500400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:45500200-45501000	Weak transcription	Aorta	Aorta
44	chr1:45500200-45501200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr1:45500200-45501600	Weak transcription	Fetal Intestine Large	intestine

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