Variant report

Variant	rs13279327
Chromosome Location	chr8:48442384-48442385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:48441687..48444204-chr8:48648313..48651863,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221869	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10094128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs10099236	0.93[JPT][hapmap];0.86[YRI][hapmap]
rs10109113	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10441557	0.87[CHD][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap]
rs10441581	0.86[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[YRI][hapmap]
rs10957370	0.90[CHD][hapmap];0.93[JPT][hapmap];0.89[LWK][hapmap];0.86[YRI][hapmap]
rs12547497	0.88[ASN][1000 genomes]
rs12674784	0.96[CEU][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs13280068	0.85[EUR][1000 genomes]
rs1542721	0.87[JPT][hapmap]
rs16930163	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs16930230	0.87[JPT][hapmap]
rs2130411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[ASN][1000 genomes]
rs4436571	0.91[ASN][1000 genomes]
rs4486659	0.82[ASN][1000 genomes]
rs4594029	0.81[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4873101	0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs4873269	0.90[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap]
rs4873386	0.93[ASN][1000 genomes]
rs4873446	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4873463	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4873478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs4873546	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.86[YRI][hapmap]
rs6472452	0.92[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap]
rs6981485	0.80[ASN][1000 genomes]
rs6986054	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[YRI][hapmap]
rs7825148	0.88[ASN][1000 genomes]
rs7827571	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[YRI][hapmap]
rs7830859	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7833589	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.80[TSI][hapmap];0.95[YRI][hapmap]
rs7842068	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs7846620	0.93[JPT][hapmap];0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1025674	chr8:48306843-48548862	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1023409	chr8:48320442-48454089	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv539595	chr8:48320442-48454089	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv890848	chr8:48405007-48535622	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv470211	chr8:48405007-48545961	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13279327	SNAI2	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48434000-48455400	Weak transcription	Primary T cells from cord blood	blood
2	chr8:48434400-48444400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr8:48436600-48445400	Weak transcription	GM12878-XiMat	blood
4	chr8:48438000-48444200	Weak transcription	NHEK	skin
5	chr8:48438000-48446400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr8:48438800-48452400	Weak transcription	HSMM	muscle
7	chr8:48439400-48442400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr8:48439600-48445000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr8:48439800-48442800	Weak transcription	Placenta	Placenta
10	chr8:48439800-48443400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr8:48439800-48455400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr8:48440000-48442400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr8:48440000-48443600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr8:48440000-48444200	Weak transcription	HepG2	liver
15	chr8:48440000-48444400	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr8:48440000-48445200	Weak transcription	Brain Hippocampus Middle	brain
17	chr8:48440000-48446400	Weak transcription	Fetal Intestine Small	intestine
18	chr8:48440000-48452600	Weak transcription	Fetal Kidney	kidney
19	chr8:48441800-48442800	Weak transcription	Small Intestine	intestine
20	chr8:48442000-48444400	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr8:48442000-48447800	Weak transcription	Primary B cells from cord blood	blood
22	chr8:48442200-48442600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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