Variant report

Variant	rs56152727
Chromosome Location	chr3:156487828-156487829
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156487583..156490581-chr3:156498612..156500239,2	MCF-7	breast:
2	chr3:156487668..156490241-chr3:156516348..156519090,2	K562	blood:
3	chr3:156479506..156481300-chr3:156485653..156488163,2	MCF-7	breast:
4	chr3:156481334..156484015-chr3:156486601..156488604,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10513495	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12636629	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1367312	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1529581	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17373227	0.88[EUR][1000 genomes]
rs344004	0.90[AMR][1000 genomes]
rs41366145	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4364127	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55686038	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55748213	0.92[ASN][1000 genomes]
rs56128116	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56245561	0.87[EUR][1000 genomes]
rs56354026	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56357051	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56836190	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56960846	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57483705	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58263861	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58822703	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59689193	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60032002	1.00[ASN][1000 genomes]
rs60178381	0.82[ASN][1000 genomes]
rs73013957	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73019737	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019748	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019749	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs891463	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919520	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56152727	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs56152727	LINC00886	cis	Thyroid	GTEx
rs56152727	LINC00886	cis	Artery Tibial	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156481000-156490400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:156481000-156490600	Weak transcription	NH-A	brain
3	chr3:156483200-156488000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:156483400-156490400	Weak transcription	HUVEC	blood vessel
5	chr3:156483600-156490200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:156483600-156490600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:156486800-156488400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:156487200-156488400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:156487200-156488400	Enhancers	HSMMtube	muscle
10	chr3:156487200-156488600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:156487200-156488600	Enhancers	NHDF-Ad	bronchial
12	chr3:156487200-156488600	Enhancers	Osteobl	bone
13	chr3:156487200-156489200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:156487400-156489200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:156487600-156488000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr3:156487600-156489200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:156487600-156489800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:156487600-156491000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:156487600-156491200	Enhancers	NHEK	skin
20	chr3:156487800-156489200	Enhancers	HMEC	breast
21	chr3:156487800-156490600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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