Variant report

Variant	rs41366145
Chromosome Location	chr3:156489722-156489723
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	chr3:156489605..156491282-chr3:156493391..156495040,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10513495	0.90[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs10513503	0.93[TSI][hapmap]
rs12632784	0.92[GIH][hapmap]
rs12636629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1367312	0.81[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1529581	0.92[EUR][1000 genomes]
rs16826869	0.93[TSI][hapmap]
rs16826877	0.93[TSI][hapmap]
rs17373227	0.81[EUR][1000 genomes]
rs186930	0.84[AMR][1000 genomes]
rs344042	0.84[AMR][1000 genomes]
rs344044	0.84[AMR][1000 genomes]
rs4364127	0.87[EUR][1000 genomes]
rs55686038	0.92[EUR][1000 genomes]
rs56128116	0.80[EUR][1000 genomes]
rs56152727	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56354026	0.84[EUR][1000 genomes]
rs56357051	0.92[EUR][1000 genomes]
rs57483705	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58263861	0.92[EUR][1000 genomes]
rs58822703	0.89[EUR][1000 genomes]
rs59689193	0.91[EUR][1000 genomes]
rs73013957	0.80[EUR][1000 genomes]
rs73019737	0.92[EUR][1000 genomes]
rs73019748	0.92[EUR][1000 genomes]
rs73019749	0.92[EUR][1000 genomes]
rs7609790	0.82[JPT][hapmap]
rs891463	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs919520	0.81[CEU][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs41366145	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs41366145	LINC00886	cis	Thyroid	GTEx
rs41366145	SMC4	cis	parietal	SCAN
rs41366145	LINC00886	cis	Artery Tibial	GTEx

Chromatin state (count:20 , 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	chr3:156483400-156490400	Weak transcription	HUVEC	blood vessel
4	chr3:156483600-156490200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:156483600-156490600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:156487600-156489800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:156487600-156491000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:156487600-156491200	Enhancers	NHEK	skin
9	chr3:156487800-156490600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:156488000-156490200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:156488400-156494400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:156488400-156494400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:156488600-156490400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:156488600-156490600	Weak transcription	NHDF-Ad	bronchial
15	chr3:156488600-156490600	Weak transcription	Osteobl	bone
16	chr3:156489200-156490400	Weak transcription	HMEC	breast
17	chr3:156489200-156490600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:156489200-156490600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:156489200-156490600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:156489200-156490600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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