Variant report

Variant	rs3821552
Chromosome Location	chr3:81702139-81702140
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:81702049-81702148	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
GBE1	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11127740	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11707026	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11710970	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs12637814	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13062741	0.91[CEU][hapmap]
rs13065281	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13072957	0.96[CEU][hapmap];0.90[YRI][hapmap];0.85[EUR][1000 genomes]
rs13073613	0.87[CEU][hapmap]
rs13079104	0.91[CEU][hapmap]
rs13080520	0.87[CEU][hapmap]
rs13086292	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13088603	0.81[EUR][1000 genomes]
rs13099615	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1464790	0.91[CEU][hapmap];0.90[YRI][hapmap]
rs2053805	0.96[CEU][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2229519	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28435942	0.87[EUR][1000 genomes]
rs3755713	0.95[CEU][hapmap];0.90[YRI][hapmap]
rs3772884	0.96[CEU][hapmap];0.90[YRI][hapmap]
rs3772896	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs3772909	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3772912	0.83[CEU][hapmap]
rs3821548	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs3821551	0.96[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3849571	0.84[CEU][hapmap]
rs3943556	0.96[CEU][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6767749	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6795133	0.95[CEU][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7618634	0.81[EUR][1000 genomes]
rs7620240	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs7634258	0.96[CEU][hapmap];0.90[YRI][hapmap];0.81[EUR][1000 genomes]
rs7642112	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9826069	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933756	chr3:81413060-81754738	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1003217	chr3:81435044-81752521	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1012133	chr3:81499082-81817471	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv933259	chr3:81523854-81730617	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv949545	chr3:81523898-81893929	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv999587	chr3:81534364-81707800	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv536603	chr3:81534364-81707800	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1009607	chr3:81651419-81825151	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv536604	chr3:81651419-81825151	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv834749	chr3:81655377-81818880	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv999992	chr3:81693662-82015969	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv536605	chr3:81693662-82015969	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv963523	chr3:81698115-81702818	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3821552	GBE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81603600-81726400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:81627400-81755000	Weak transcription	Primary B cells from cord blood	blood
3	chr3:81642000-81753000	Weak transcription	HUVEC	blood vessel
4	chr3:81642200-81712200	Weak transcription	Ovary	ovary
5	chr3:81662200-81703000	Weak transcription	HSMMtube	muscle
6	chr3:81680600-81703000	Weak transcription	Hela-S3	cervix
7	chr3:81682400-81706600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:81684400-81712400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:81689000-81712200	Weak transcription	Lung	lung
10	chr3:81689600-81712200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:81689600-81726200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:81689600-81744000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:81689800-81744000	Weak transcription	Right Ventricle	heart
14	chr3:81693000-81726800	Weak transcription	GM12878-XiMat	blood
15	chr3:81694000-81707800	Weak transcription	HepG2	liver
16	chr3:81695200-81748000	Weak transcription	Aorta	Aorta
17	chr3:81695400-81733800	Weak transcription	HSMM	muscle
18	chr3:81695400-81746200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:81695600-81728400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:81699200-81704400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:81699200-81709600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:81699200-81712400	Weak transcription	Adipose Nuclei	Adipose
23	chr3:81699200-81715600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:81699200-81717400	Weak transcription	NHDF-Ad	bronchial
25	chr3:81699400-81707400	Weak transcription	Liver	Liver
26	chr3:81699400-81766000	Weak transcription	NHLF	lung
27	chr3:81701200-81705200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:81701400-81702800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:81701400-81704600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:81701400-81704800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:81701400-81705400	Weak transcription	Psoas Muscle	Psoas
32	chr3:81701400-81712200	Weak transcription	Left Ventricle	heart
33	chr3:81701600-81703400	Weak transcription	Dnd41	blood
34	chr3:81701600-81705400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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