Variant report

Variant	rs344045
Chromosome Location	chr3:156481051-156481052
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156478908..156481855-chr3:156482060..156485286,3	MCF-7	breast:
2	chr3:156479506..156481300-chr3:156485653..156488163,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1430408	0.93[ASN][1000 genomes]
rs186930	0.96[ASN][1000 genomes]
rs2043108	0.90[ASN][1000 genomes]
rs344025	0.81[ASN][1000 genomes]
rs344026	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs344042	1.00[ASN][1000 genomes]
rs344044	0.99[ASN][1000 genomes]
rs344046	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810308	0.81[EUR][1000 genomes]
rs9822953	0.84[JPT][hapmap]
rs9838430	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs344045	B3GALNT1	cis	cerebellum	SCAN
rs344045	LINC00886	cis	Heart Left Ventricle	GTEx
rs344045	SMC4	cis	parietal	SCAN
rs344045	TRIM59	cis	cerebellum	SCAN
rs344045	LINC00886	cis	Thyroid	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156477800-156481200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:156477800-156481200	Enhancers	NHEK	skin
3	chr3:156478000-156482200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:156478000-156483400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:156478000-156483800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr3:156478200-156481200	Enhancers	Osteobl	bone
7	chr3:156478200-156483600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:156478800-156481200	Enhancers	Fetal Stomach	stomach
9	chr3:156479200-156481600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:156479400-156481800	Weak transcription	GM12878-XiMat	blood
11	chr3:156479400-156483200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:156480200-156481400	Weak transcription	K562	blood
13	chr3:156480400-156481600	Enhancers	NHDF-Ad	bronchial
14	chr3:156480400-156482000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:156480800-156481200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:156480800-156481800	Weak transcription	NHLF	lung
17	chr3:156480800-156482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:156481000-156481800	Weak transcription	Fetal Lung	lung
19	chr3:156481000-156481800	Weak transcription	HSMM	muscle
20	chr3:156481000-156482000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:156481000-156482000	Enhancers	Colon Smooth Muscle	Colon
22	chr3:156481000-156482400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:156481000-156482400	Weak transcription	HMEC	breast
24	chr3:156481000-156482600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:156481000-156483000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:156481000-156485400	Weak transcription	HSMMtube	muscle
27	chr3:156481000-156490400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:156481000-156490600	Weak transcription	NH-A	brain

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