Variant report

Variant	rs1012583
Chromosome Location	chr3:150087008-150087009
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150068040..150070042-chr3:150085937..150088892,3	MCF-7	breast:
2	chr3:150086902..150089689-chr3:150137707..150139758,2	MCF-7	breast:
3	chr3:150086313..150087997-chr3:150093926..150095671,2	MCF-7	breast:
4	chr3:150081211..150094856-chr3:150124384..150132921,41	MCF-7	breast:
5	chr3:150086685..150087637-chr3:150126106..150126862,2	MCF-7	breast:
6	chr3:150081035..150094397-chr3:150122156..150134666,40	MCF-7	breast:
7	chr3:150086784..150089218-chr3:150089694..150091385,2	MCF-7	breast:
8	chr3:150081232..150084545-chr3:150085072..150089813,5	K562	blood:
9	chr3:150086785..150088735-chr3:150127952..150130742,2	K562	blood:
10	chr3:150031134..150033723-chr3:150086992..150089751,2	MCF-7	breast:
11	chr3:150086519..150091866-chr3:150093461..150097312,5	K562	blood:
12	chr3:149953883..149958002-chr3:150086576..150089576,4	MCF-7	breast:
13	chr3:150061806..150067641-chr3:150085085..150089827,11	MCF-7	breast:
14	chr3:149954498..149958099-chr3:150086943..150091403,7	MCF-7	breast:
15	chr3:150086925..150089531-chr3:150177059..150179337,2	K562	blood:
16	chr3:150082769..150087099-chr3:150088300..150090870,4	K562	blood:
17	chr3:150086378..150089997-chr3:150256465..150259602,3	MCF-7	breast:
18	chr3:150071761..150072318-chr3:150086669..150087193,3	MCF-7	breast:
19	chr3:150033113..150037399-chr3:150086580..150091176,6	MCF-7	breast:
20	chr3:150081232..150084840-chr3:150085072..150088254,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196428	Chromatin interaction
ENSG00000244541	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12485291	0.91[JPT][hapmap]
rs12489388	0.90[ASN][1000 genomes]
rs12493174	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59663142	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73163688	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829755	chr3:149992023-150156001	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
IgG glycosylation	23382691	GWAS catalog

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150081200-150088200	Weak transcription	Stomach Mucosa	stomach
2	chr3:150082400-150089400	Weak transcription	HepG2	liver
3	chr3:150083200-150088000	Weak transcription	Esophagus	oesophagus
4	chr3:150083200-150088200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:150083200-150088200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:150083600-150087200	Weak transcription	HSMMtube	muscle
7	chr3:150083800-150087400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:150083800-150087400	Weak transcription	NH-A	brain
9	chr3:150084000-150087800	Weak transcription	HSMM	muscle
10	chr3:150084600-150087800	Weak transcription	Fetal Kidney	kidney
11	chr3:150084600-150088000	Weak transcription	Right Atrium	heart
12	chr3:150085000-150087600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr3:150085200-150087800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:150085200-150088000	Enhancers	Hela-S3	cervix
15	chr3:150085400-150088000	Enhancers	NHDF-Ad	bronchial
16	chr3:150085600-150087400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:150085600-150088000	Enhancers	Osteobl	bone
18	chr3:150085800-150088800	Enhancers	Placenta	Placenta
19	chr3:150086000-150087200	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:150086000-150087400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:150086000-150087600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:150086000-150087800	Weak transcription	Fetal Lung	lung
23	chr3:150086200-150087200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:150086200-150087800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:150086200-150102200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:150086400-150087600	Enhancers	A549	lung
27	chr3:150086600-150087200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:150086600-150087200	Enhancers	K562	blood
29	chr3:150086600-150087600	Enhancers	HUVEC	blood vessel
30	chr3:150086600-150087800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:150086600-150087800	Enhancers	NHEK	skin
32	chr3:150086600-150088000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:150086600-150088000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:150086800-150087400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:150086800-150087800	Enhancers	HMEC	breast
36	chr3:150086800-150088000	Enhancers	Muscle Satellite Cultured Cells	--
37	chr3:150087000-150087600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:150087000-150087600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:150087000-150087800	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr3:150087000-150088000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:150087000-150088000	Weak transcription	NHLF	lung
42	chr3:150087000-150088200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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