Variant report

Variant	rs4129893
Chromosome Location	chr8:119518190-119518191
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:119506168..119508828-chr8:119515870..119518341,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12674772	0.88[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs12682339	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34696241	0.93[ASN][1000 genomes]
rs4242582	0.88[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs4242583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4242585	0.89[ASN][1000 genomes]
rs4421377	0.88[CHB][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4514016	0.85[YRI][hapmap]
rs4551393	0.88[CHB][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4557731	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs4876851	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4876852	0.84[JPT][hapmap]
rs56078225	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56151246	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56306005	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62531882	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62531887	0.93[ASN][1000 genomes]
rs7015005	0.84[JPT][hapmap]

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	nsv1032681	chr8:119153316-119609948	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv539737	chr8:119153316-119609948	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv831443	chr8:119390590-119590662	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4129893	TNFRSF11B	cis	parietal	SCAN
rs4129893	SLC14A2	trans	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:119502000-119522400	Weak transcription	Pancreas	Pancrea
2	chr8:119507600-119518600	Weak transcription	Fetal Lung	lung
3	chr8:119516600-119518200	Flanking Active TSS	GM12878-XiMat	blood
4	chr8:119516800-119518400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr8:119516800-119520000	Enhancers	Stomach Mucosa	stomach
6	chr8:119517000-119519200	Enhancers	NHLF	lung
7	chr8:119517000-119520200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr8:119517000-119522800	Enhancers	HMEC	breast
9	chr8:119517200-119519200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr8:119517200-119520400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr8:119517200-119522800	Enhancers	NHEK	skin
12	chr8:119517600-119518200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr8:119517600-119519800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr8:119517800-119518200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr8:119517800-119519000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr8:119518000-119518400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr8:119518000-119518800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr8:119518000-119519000	Enhancers	Liver	Liver
19	chr8:119518000-119519200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr8:119518000-119519200	Weak transcription	Osteobl	bone
21	chr8:119518000-119519800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr8:119518000-119520000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr8:119518000-119520000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr8:119518000-119522800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links