Variant report

Variant	rs39519
Chromosome Location	chr8:90846042-90846043
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153928343..153930810-chr8:90845808..90848291,2	MCF-7	breast:
2	chr8:90845301..90847765-chr8:90850348..90853325,2	MCF-7	breast:
3	chr8:90838601..90840941-chr8:90843850..90846321,2	MCF-7	breast:
4	chr8:90843753..90846365-chr8:90914514..90916042,2	MCF-7	breast:
5	chr8:90844504..90846119-chr8:90995493..90997687,2	MCF-7	breast:
6	chr8:90844734..90847246-chr8:90847760..90849982,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160741	Chromatin interaction
ENSG00000104320	Chromatin interaction
ENSG00000164823	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs365871	0.91[ASN][1000 genomes]
rs369771	0.89[JPT][hapmap];0.87[YRI][hapmap]
rs374957	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs386857	0.89[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs394108	0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs39515	0.83[JPT][hapmap];0.87[YRI][hapmap]
rs39768	0.91[AFR][1000 genomes]
rs39771	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs39772	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398959	0.89[ASN][1000 genomes]
rs400571	0.90[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40250	0.93[EUR][1000 genomes]
rs40459	0.92[CEU][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs410577	0.90[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs410663	0.92[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs418634	0.89[EUR][1000 genomes]
rs419890	0.93[EUR][1000 genomes]
rs42186	0.92[EUR][1000 genomes]
rs42481	0.92[CEU][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs425312	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs426240	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs427854	0.92[EUR][1000 genomes]
rs43136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs43229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447989	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs454561	0.89[JPT][hapmap];0.87[YRI][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	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv891182	chr8:90785685-90888786	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv520356	chr8:90823687-90857989	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv2761448	chr8:90837630-90853986	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs39519	CALB1	cis	cerebellum	SCAN
rs39519	SLC29A4	trans	cerebellum	SCAN
rs39519	TMEM100	trans	parietal	SCAN
rs39519	RIPK2	cis	cerebellum	SCAN
rs39519	OSGIN2	cis	parietal	SCAN
rs39519	MMP16	cis	cerebellum	SCAN
rs39519	RP11-37B2.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90837000-90847600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr8:90839200-90848400	Weak transcription	Osteobl	bone
3	chr8:90840000-90847400	Weak transcription	A549	lung
4	chr8:90845000-90847600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr8:90845800-90846200	Flanking Active TSS	NHDF-Ad	bronchial
6	chr8:90845800-90846200	Active TSS	NHLF	lung
7	chr8:90845800-90846600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr8:90845800-90846600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr8:90845800-90848000	Flanking Active TSS	GM12878-XiMat	blood
10	chr8:90845800-90850200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr8:90846000-90846200	Enhancers	Primary B cells from peripheral blood	blood
12	chr8:90846000-90846200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr8:90846000-90846200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr8:90846000-90846800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr8:90846000-90850400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr8:90846000-90850600	Enhancers	Primary T helper cells PMA-I stimulated	--

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