Variant report

Variant	rs1881918
Chromosome Location	chr3:133171284-133171285
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:133169398..133190840-chr3:133288286..133298861,41	MCF-7	breast:
2	chr3:133165936..133167701-chr3:133170915..133173583,2	MCF-7	breast:
3	chr3:133170643..133173658-chr3:133173707..133177209,4	MCF-7	breast:
4	chr3:133169681..133172224-chr3:133173356..133176269,2	K562	blood:
5	chr3:133170213..133174135-chr3:133291301..133294544,7	MCF-7	breast:
6	chr3:133162344..133164568-chr3:133170486..133172340,2	MCF-7	breast:
7	chr3:133143999..133146404-chr3:133171252..133173491,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249993	Chromatin interaction
ENSG00000091527	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10935064	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11715830	0.89[ASN][1000 genomes]
rs13069027	0.90[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs2078262	0.81[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs2276737	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2737717	0.95[CHB][hapmap]
rs2859679	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7612063	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs931099	0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877504	chr3:133122216-133172374	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1007047	chr3:133137664-133181388	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1006289	chr3:133137664-133186808	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1829199	chr3:133158065-133213047	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv877505	chr3:133167363-133235272	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1881918	BFSP2	cis	lymphoblastoid	seeQTL
rs1881918	TF	cis	parietal	SCAN
rs1881918	SOX14	cis	cerebellum	SCAN
rs1881918	FAIM	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133161000-133191000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:133165400-133178600	Weak transcription	Aorta	Aorta
3	chr3:133167600-133172400	Weak transcription	Gastric	stomach
4	chr3:133167800-133171400	Weak transcription	Placenta	Placenta
5	chr3:133168000-133171400	Weak transcription	Fetal Lung	lung
6	chr3:133168000-133172200	Weak transcription	Stomach Mucosa	stomach
7	chr3:133168200-133171800	Weak transcription	Brain Germinal Matrix	brain
8	chr3:133168200-133171800	Weak transcription	Brain Substantia Nigra	brain
9	chr3:133168200-133178800	Weak transcription	Fetal Kidney	kidney
10	chr3:133169400-133177400	Weak transcription	Thymus	Thymus
11	chr3:133169800-133179400	Weak transcription	GM12878-XiMat	blood
12	chr3:133170200-133172600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:133170200-133173200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:133170400-133177200	Weak transcription	Fetal Thymus	thymus
15	chr3:133170800-133173000	Enhancers	HepG2	liver
16	chr3:133170800-133173200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr3:133171000-133172400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:133171000-133172400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:133171000-133172600	Enhancers	Liver	Liver
20	chr3:133171000-133172800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:133171200-133171400	Flanking Active TSS	A549	lung
22	chr3:133171200-133171600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:133171200-133171600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:133171200-133171600	Enhancers	Fetal Stomach	stomach
25	chr3:133171200-133172200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr3:133171200-133172400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:133171200-133172400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:133171200-133172400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr3:133171200-133172400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:133171200-133173400	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links