Variant report

Variant	rs344042
Chromosome Location	chr3:156481537-156481538
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156481334..156484015-chr3:156486601..156488604,3	MCF-7	breast:
2	chr3:156478908..156481855-chr3:156482060..156485286,3	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs12636629	0.84[AMR][1000 genomes]
rs1430408	0.93[ASN][1000 genomes]
rs186930	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2043108	0.90[ASN][1000 genomes]
rs344025	0.81[ASN][1000 genomes]
rs344026	0.83[ASN][1000 genomes]
rs344044	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs344045	1.00[ASN][1000 genomes]
rs344046	1.00[ASN][1000 genomes]
rs41366145	0.84[AMR][1000 genomes]
rs57483705	0.84[AMR][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs344042	LINC00886	cis	Esophagus Muscularis	GTEx
rs344042	LINC00886	cis	Esophagus Mucosa	GTEx
rs344042	LINC00886	cis	Thyroid	GTEx
rs344042	LINC00886	cis	Heart Left Ventricle	GTEx
rs344042	LINC00886	cis	Artery Tibial	GTEx
rs344042	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:27 , 50 per page) page: 1

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

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