Variant report

Variant	rs3772882
Chromosome Location	chr3:81808602-81808603
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:81784646..81786300-chr3:81807469..81810192,2	MCF-7	breast:
2	chr3:81807656..81810555-chr3:81826584..81828101,2	MCF-7	breast:
3	chr3:81806041..81808024-chr3:81808030..81809607,2	K562	blood:
4	chr3:81532629..81534291-chr3:81807934..81809803,2	MCF-7	breast:
5	chr3:81789819..81797196-chr3:81807650..81813820,9	K562	blood:
6	chr3:81807474..81810445-chr3:81824019..81825823,3	K562	blood:

Variant related genes	Relation type
ENSG00000114480	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11127740	0.80[CEU][hapmap]
rs11707026	0.83[TSI][hapmap]
rs11710970	0.91[CEU][hapmap]
rs11711331	0.96[CEU][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs11915042	0.83[EUR][1000 genomes]
rs13072957	0.80[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs13073613	0.82[GIH][hapmap]
rs13079104	0.82[GIH][hapmap]
rs13080520	0.87[GIH][hapmap];0.89[TSI][hapmap]
rs13088000	0.83[EUR][1000 genomes]
rs1375086	0.84[GIH][hapmap]
rs1464790	0.82[GIH][hapmap]
rs2053805	0.80[CEU][hapmap];0.80[GIH][hapmap];0.81[TSI][hapmap]
rs2290081	0.87[EUR][1000 genomes]
rs2594547	0.87[GIH][hapmap]
rs2594551	0.87[GIH][hapmap]
rs2594562	0.87[GIH][hapmap]
rs2680245	0.87[GIH][hapmap]
rs2691093	0.84[GIH][hapmap]
rs3755713	0.83[GIH][hapmap]
rs3772883	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772884	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs3772896	0.91[CEU][hapmap]
rs3772912	0.96[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs3821548	0.92[CEU][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap]
rs3821551	0.80[CEU][hapmap]
rs3849570	0.96[CEU][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap]
rs3849571	0.92[CEU][hapmap]
rs3860595	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4411908	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6548773	0.83[EUR][1000 genomes]
rs6795133	0.82[GIH][hapmap];0.81[TSI][hapmap]
rs6803932	0.87[GIH][hapmap]
rs7620240	0.92[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs7634258	0.80[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs9817181	0.84[EUR][1000 genomes]
rs9818006	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9826270	0.83[EUR][1000 genomes]
rs9842330	0.84[EUR][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
rs3772882	GBE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81781000-81809400	Weak transcription	Primary B cells from peripheral blood	blood
2	chr3:81791200-81808800	Weak transcription	Primary T cells from cord blood	blood
3	chr3:81792000-81810200	Weak transcription	Spleen	Spleen
4	chr3:81793000-81809600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:81793200-81809200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:81793800-81809200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:81793800-81810000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:81795600-81810000	Weak transcription	Lung	lung
9	chr3:81796200-81809200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:81796800-81809200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:81797400-81809800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:81798400-81809000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr3:81799400-81809400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:81799800-81809800	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:81800400-81809400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:81800400-81809400	Weak transcription	Brain Angular Gyrus	brain
17	chr3:81800800-81809400	Weak transcription	Brain Substantia Nigra	brain
18	chr3:81801800-81809200	Weak transcription	Fetal Intestine Small	intestine
19	chr3:81802800-81809000	ZNF genes & repeats	GM12878-XiMat	blood
20	chr3:81803400-81809800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr3:81804200-81809200	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:81804200-81809800	Weak transcription	Esophagus	oesophagus
23	chr3:81804600-81808800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:81804600-81808800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:81805000-81809400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:81805400-81808800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:81805600-81808800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:81805600-81811600	Active TSS	Right Ventricle	heart
29	chr3:81805800-81809600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:81806400-81808800	ZNF genes & repeats	A549	lung
31	chr3:81806400-81810000	Transcr. at gene 5' and 3'	Dnd41	blood
32	chr3:81806600-81809600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:81806600-81809800	Weak transcription	Ovary	ovary
34	chr3:81806800-81808800	Weak transcription	Aorta	Aorta
35	chr3:81806800-81809600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:81806800-81811000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:81807000-81808800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr3:81807000-81808800	Genic enhancers	HSMM	muscle
39	chr3:81807000-81809000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:81807200-81809400	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr3:81807200-81809400	Enhancers	NH-A	brain
42	chr3:81807200-81809600	Weak transcription	Placenta	Placenta
43	chr3:81807400-81809200	Weak transcription	Primary B cells from cord blood	blood
44	chr3:81807600-81808800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:81807600-81810000	Weak transcription	Gastric	stomach
46	chr3:81807800-81808800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:81807800-81809200	Weak transcription	Colon Smooth Muscle	Colon
48	chr3:81807800-81811600	Active TSS	Psoas Muscle	Psoas
49	chr3:81808000-81809000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:81808000-81809000	Weak transcription	Monocytes-CD14+_RO01746	blood

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