Variant report

Variant	rs3849570
Chromosome Location	chr3:81792112-81792113
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:81789146..81795604-chr3:81809193..81811958,7	MCF-7	breast:
2	chr3:81789819..81797196-chr3:81807650..81813820,9	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	0.84[CEU][hapmap]
rs11707026	0.85[CHD][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs11710970	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs11711331	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs13072957	0.84[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.97[TSI][hapmap]
rs13073613	0.86[GIH][hapmap];0.82[TSI][hapmap]
rs13079104	0.86[GIH][hapmap];0.82[TSI][hapmap]
rs13080520	0.82[GIH][hapmap]
rs13099615	0.84[CEU][hapmap]
rs1375086	0.80[GIH][hapmap]
rs1464790	0.82[CHB][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap]
rs2053805	0.84[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap]
rs2229519	0.85[CHD][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap]
rs2594547	0.83[GIH][hapmap]
rs2594551	0.83[GIH][hapmap]
rs2594562	0.83[GIH][hapmap]
rs2680245	0.83[GIH][hapmap]
rs2691093	0.89[GIH][hapmap]
rs3755713	0.83[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap]
rs3772882	0.96[CEU][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap]
rs3772883	0.96[CEU][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap]
rs3772884	0.84[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.97[TSI][hapmap]
rs3772891	0.88[TSI][hapmap]
rs3772896	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3772899	0.84[GIH][hapmap]
rs3772902	0.82[GIH][hapmap]
rs3772912	0.96[CEU][hapmap];0.84[GIH][hapmap]
rs3821548	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3821551	0.84[CEU][hapmap]
rs3849571	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3860595	0.96[CEU][hapmap];0.91[GIH][hapmap]
rs3943556	0.83[CEU][hapmap]
rs4411908	0.96[CEU][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap]
rs6795133	0.83[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.97[TSI][hapmap]
rs6803932	0.83[GIH][hapmap]
rs7618973	0.82[MEX][hapmap]
rs7620240	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]
rs7634258	0.84[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.97[TSI][hapmap]
rs9845467	0.82[MEX][hapmap]

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
rs3849570	GBE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81727200-81792200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:81773200-81792200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:81776000-81807400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:81781000-81792200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr3:81781000-81809400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr3:81782200-81800400	Weak transcription	Primary B cells from cord blood	blood
7	chr3:81782400-81800200	Weak transcription	Left Ventricle	heart
8	chr3:81782800-81796600	Weak transcription	Right Atrium	heart
9	chr3:81784800-81792800	Weak transcription	HepG2	liver
10	chr3:81785200-81793000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:81785600-81793000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:81788600-81792600	Strong transcription	Dnd41	blood
13	chr3:81789000-81792200	Weak transcription	Fetal Lung	lung
14	chr3:81789200-81794400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:81789600-81793600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:81789600-81794400	Enhancers	Fetal Heart	heart
17	chr3:81789600-81794600	Enhancers	Hela-S3	cervix
18	chr3:81789600-81794800	Enhancers	Adipose Nuclei	Adipose
19	chr3:81790000-81793400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:81790600-81792400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:81790600-81792600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:81790600-81793200	Enhancers	Colon Smooth Muscle	Colon
23	chr3:81790800-81792800	Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr3:81791000-81793400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:81791200-81792200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr3:81791200-81792200	Flanking Active TSS	A549	lung
27	chr3:81791200-81793800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:81791200-81794800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:81791200-81794800	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr3:81791200-81794800	Enhancers	Liver	Liver
31	chr3:81791200-81808800	Weak transcription	Primary T cells from cord blood	blood
32	chr3:81791400-81792400	Active TSS	HSMMtube	muscle
33	chr3:81791400-81795400	Weak transcription	Right Ventricle	heart
34	chr3:81791400-81796400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:81791600-81792200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:81791600-81792200	Active TSS	Aorta	Aorta
37	chr3:81791600-81792200	Flanking Active TSS	HMEC	breast
38	chr3:81791600-81792400	Flanking Active TSS	NH-A	brain
39	chr3:81791600-81792400	Flanking Active TSS	NHEK	skin
40	chr3:81791600-81792800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:81791600-81793200	Enhancers	Rectal Smooth Muscle	rectum
42	chr3:81791600-81793400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:81791600-81794400	Enhancers	K562	blood
44	chr3:81791600-81803400	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:81791800-81792200	Flanking Active TSS	Ovary	ovary
46	chr3:81791800-81792200	Flanking Active TSS	NHDF-Ad	bronchial
47	chr3:81791800-81792200	Flanking Active TSS	Osteobl	bone
48	chr3:81791800-81792600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:81791800-81792600	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr3:81791800-81792600	Active TSS	Skeletal Muscle Female	skeletal muscle

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