Variant report

Variant	rs7620240
Chromosome Location	chr3:81762787-81762788
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:81760914..81764282-chr3:81767047..81769865,3	K562	blood:
2	chr3:81754177..81756278-chr3:81762683..81765640,2	K562	blood:
3	chr3:81760914..81763502-chr3:81767047..81769294,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11127740	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs11707026	0.83[CEU][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs11710970	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11711331	0.94[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12637814	0.88[EUR][1000 genomes]
rs13062741	0.82[CEU][hapmap]
rs13065281	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs13072957	0.88[CEU][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs13073613	0.84[GIH][hapmap];0.82[TSI][hapmap]
rs13079104	0.83[CEU][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs13086292	0.86[EUR][1000 genomes]
rs13099615	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs13340130	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464790	0.83[CEU][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap]
rs2053805	0.88[CEU][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs2229519	0.83[CEU][hapmap];0.87[CHD][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs2594547	0.81[GIH][hapmap]
rs2594551	0.81[GIH][hapmap]
rs2594562	0.81[GIH][hapmap]
rs2680245	0.81[GIH][hapmap]
rs2691093	0.86[GIH][hapmap]
rs28435942	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34692099	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3755713	0.87[CEU][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.94[TSI][hapmap]
rs3772882	0.92[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs3772883	0.92[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs3772884	0.88[CEU][hapmap];0.82[CHD][hapmap];0.97[TSI][hapmap]
rs3772891	0.88[TSI][hapmap]
rs3772896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772899	0.82[GIH][hapmap]
rs3772909	0.87[EUR][1000 genomes]
rs3772912	0.91[CEU][hapmap];0.82[GIH][hapmap];0.80[EUR][1000 genomes]
rs3821548	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821551	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs3821552	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs3849570	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3849571	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3860595	0.92[CEU][hapmap];0.89[GIH][hapmap]
rs3943556	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs4411908	0.92[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs6767749	0.90[EUR][1000 genomes]
rs6795133	0.87[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs6803932	0.81[GIH][hapmap]
rs7618634	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7618973	0.83[MEX][hapmap]
rs7634258	0.88[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap]
rs7642112	0.83[CEU][hapmap]
rs9826069	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7620240	GBE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81699400-81766000	Weak transcription	NHLF	lung
2	chr3:81714400-81763600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:81726800-81766200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:81727200-81792200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:81732000-81766400	Weak transcription	HSMMtube	muscle
6	chr3:81734600-81765800	Weak transcription	HepG2	liver
7	chr3:81735600-81764200	Weak transcription	A549	lung
8	chr3:81744200-81772800	Weak transcription	Right Ventricle	heart
9	chr3:81747000-81764000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:81749000-81764000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:81749200-81772800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:81749400-81766000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:81749400-81766000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:81749400-81766000	Weak transcription	Adipose Nuclei	Adipose
15	chr3:81750200-81772600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:81753200-81763800	Weak transcription	Liver	Liver
17	chr3:81754400-81766000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:81754800-81766000	Weak transcription	NHDF-Ad	bronchial
19	chr3:81755600-81763800	Weak transcription	Left Ventricle	heart
20	chr3:81755600-81764000	Weak transcription	Pancreas	Pancrea
21	chr3:81755600-81766000	Weak transcription	Gastric	stomach
22	chr3:81755800-81766000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:81755800-81772800	Weak transcription	Right Atrium	heart
24	chr3:81755800-81781000	Weak transcription	Primary B cells from cord blood	blood
25	chr3:81759200-81766000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:81760800-81772200	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:81761600-81766200	Weak transcription	Stomach Mucosa	stomach
28	chr3:81762000-81762800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:81762000-81764400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:81762000-81764600	Weak transcription	Placenta	Placenta
31	chr3:81762200-81762800	Enhancers	Fetal Intestine Small	intestine
32	chr3:81762200-81763200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:81762200-81764600	Strong transcription	Dnd41	blood
34	chr3:81762600-81764400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:81762600-81764800	Weak transcription	Fetal Lung	lung
36	chr3:81762600-81765800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:81762600-81766000	Weak transcription	Aorta	Aorta
38	chr3:81762600-81766000	Weak transcription	Psoas Muscle	Psoas
39	chr3:81762600-81766000	Weak transcription	HSMM	muscle
40	chr3:81762600-81766000	Weak transcription	K562	blood
41	chr3:81762600-81766000	Weak transcription	Osteobl	bone
42	chr3:81762600-81772200	Weak transcription	HUVEC	blood vessel

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