Variant report

Variant	rs3860595
Chromosome Location	chr3:81811784-81811785
allele	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	chr3:81809125-81813460	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:81810037-81811836	GM12891	blood:	n/a	n/a
3	CTCF	chr3:81811760-81811910	HFF-Myc	foreskin:	n/a	n/a
4	MYC	chr3:81809659-81811873	A549	lung:	n/a	chr3:81810948-81810964 chr3:81810392-81810402 chr3:81810858-81810868
5	POLR2A	chr3:81809196-81812982	GM12891	blood:	n/a	n/a
6	POLR2A	chr3:81808535-81812327	MCF10A-Er-Src	breast:	n/a	n/a
7	EP300	chr3:81810039-81811931	K562	blood:	n/a	chr3:81810803-81810819 chr3:81811589-81811603 chr3:81810319-81810335 chr3:81810939-81810955
8	POLR2A	chr3:81809916-81811923	GM12892	blood:	n/a	n/a
9	POLR2A	chr3:81809830-81811942	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:81809258-81811955	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr3:81809755-81811870	GM12892	blood:	n/a	n/a
12	CTCF	chr3:81809577-81811811	A549	lung:	n/a	chr3:81810955-81810968 chr3:81810858-81810871 chr3:81810953-81810971
13	POLR2A	chr3:81809393-81812042	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr3:81808053-81811812	GM12878	blood:	n/a	n/a
15	STAT3	chr3:81809837-81811803	GM12878	blood:	n/a	n/a
16	PML	chr3:81809703-81812388	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:81809088-81811920	U87	brain:	n/a	n/a
18	POLR2A	chr3:81808676-81812699	K562	blood:	n/a	n/a
19	POLR2A	chr3:81809733-81811821	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:81809950-81811846	K562	blood:	n/a	n/a
21	MTA3	chr3:81809107-81812010	GM12878	blood:	n/a	n/a
22	IRF1	chr3:81811419-81812030	K562	blood:	n/a	chr3:81811590-81811599
23	POLR2A	chr3:81809042-81811944	U87	brain:	n/a	n/a
24	BCLAF1	chr3:81809434-81811914	GM12878	blood:	n/a	chr3:81810803-81810812 chr3:81810798-81810811
25	POLR2A	chr3:81809619-81812556	GM12892	blood:	n/a	n/a
26	POLR2A	chr3:81809042-81811950	U87	brain:	n/a	n/a
27	POLR2A	chr3:81809977-81811899	GM12891	blood:	n/a	n/a
28	GATA1	chr3:81809835-81812043	PBDE	blood:	n/a	chr3:81810197-81810206 chr3:81811002-81811012 chr3:81811569-81811585 chr3:81810787-81810795
29	POLR2A	chr3:81809995-81811817	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:81789146..81795604-chr3:81809193..81811958,7	MCF-7	breast:
2	chr12:121733110..121736069-chr3:81809721..81812341,2	MCF-7	breast:
3	chr3:81789819..81797196-chr3:81807650..81813820,9	K562	blood:

Variant related genes	Relation type
GBE1	TF binding region
ENSG00000110931	Chromatin interaction
ENSG00000114480	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11127740	0.80[CEU][hapmap]
rs11710970	0.91[CEU][hapmap]
rs11711331	0.96[CEU][hapmap];0.91[GIH][hapmap];0.85[EUR][1000 genomes]
rs11915042	0.83[EUR][1000 genomes]
rs13072957	0.80[CEU][hapmap]
rs13080520	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs13088000	0.83[EUR][1000 genomes]
rs13099615	0.80[CEU][hapmap]
rs1375086	0.89[GIH][hapmap]
rs2053805	0.80[CEU][hapmap]
rs2290081	0.85[EUR][1000 genomes]
rs2594547	0.91[GIH][hapmap]
rs2594551	0.91[GIH][hapmap]
rs2594562	0.91[GIH][hapmap]
rs2680245	0.91[GIH][hapmap]
rs3772882	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]
rs3772883	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772884	0.80[CEU][hapmap]
rs3772896	0.91[CEU][hapmap]
rs3772899	0.84[GIH][hapmap]
rs3772902	0.82[GIH][hapmap]
rs3772912	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs3821548	0.92[CEU][hapmap];0.91[GIH][hapmap]
rs3821551	0.80[CEU][hapmap]
rs3849570	0.96[CEU][hapmap];0.91[GIH][hapmap]
rs3849571	0.92[CEU][hapmap]
rs4411908	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6548773	0.83[EUR][1000 genomes]
rs6803932	0.91[GIH][hapmap]
rs7620240	0.92[CEU][hapmap];0.89[GIH][hapmap]
rs7634258	0.80[CEU][hapmap]
rs9817181	0.84[EUR][1000 genomes]
rs9818006	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[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
rs3860595	GBE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81809000-81811800	Active TSS	Aorta	Aorta
2	chr3:81809600-81811800	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr3:81810200-81811800	Active TSS	Fetal Kidney	kidney
4	chr3:81810800-81811800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:81810800-81811800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:81810800-81811800	Flanking Active TSS	Dnd41	blood
7	chr3:81811000-81811800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:81811000-81811800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:81811000-81811800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr3:81811000-81811800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr3:81811000-81811800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:81811000-81811800	Flanking Active TSS	GM12878-XiMat	blood
13	chr3:81811000-81811800	Flanking Active TSS	NH-A	brain
14	chr3:81811000-81811800	Flanking Active TSS	NHDF-Ad	bronchial
15	chr3:81811000-81811800	Flanking Active TSS	Osteobl	bone
16	chr3:81811200-81811800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:81811200-81811800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr3:81811200-81811800	Flanking Active TSS	A549	lung
19	chr3:81811200-81811800	Flanking Active TSS	K562	blood
20	chr3:81811200-81812400	Enhancers	Brain Germinal Matrix	brain
21	chr3:81811200-81818200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:81811400-81811800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr3:81811400-81811800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:81811400-81811800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:81811400-81811800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:81811400-81811800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr3:81811400-81811800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:81811400-81811800	Enhancers	Brain Cingulate Gyrus	brain
29	chr3:81811400-81811800	Enhancers	Fetal Muscle Leg	muscle
30	chr3:81811400-81811800	Enhancers	Fetal Thymus	thymus
31	chr3:81811400-81811800	Enhancers	Rectal Smooth Muscle	rectum
32	chr3:81811400-81811800	Enhancers	Thymus	Thymus
33	chr3:81811400-81811800	Enhancers	NHEK	skin
34	chr3:81811400-81812000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:81811400-81812200	Weak transcription	Left Ventricle	heart
36	chr3:81811400-81812200	Enhancers	HSMM	muscle
37	chr3:81811400-81812400	Enhancers	Liver	Liver
38	chr3:81811400-81813800	Weak transcription	Right Atrium	heart
39	chr3:81811400-81818200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:81811600-81811800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:81811600-81811800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:81811600-81811800	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr3:81811600-81811800	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr3:81811600-81811800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr3:81811600-81811800	Enhancers	Primary hematopoietic stem cells	blood
46	chr3:81811600-81811800	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr3:81811600-81811800	Enhancers	Muscle Satellite Cultured Cells	--
48	chr3:81811600-81811800	Enhancers	Adipose Nuclei	Adipose
49	chr3:81811600-81811800	Enhancers	Brain Hippocampus Middle	brain
50	chr3:81811600-81811800	Enhancers	Colon Smooth Muscle	Colon

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