Variant report

Variant	rs10878376
Chromosome Location	chr12:66480440-66480441
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	chr12:66478426..66481404-chr12:66482324..66484418,3	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10431571	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10506478	0.88[CEU][hapmap]
rs10735933	0.81[CHB][hapmap]
rs10878375	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10878381	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs10878382	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs10878383	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs10878389	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap]
rs11176035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176043	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs11176056	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs11176081	0.92[YRI][hapmap]
rs12832926	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap]
rs17767200	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap]
rs1898304	0.96[CEU][hapmap];0.95[CHB][hapmap]
rs2178486	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap]
rs2870781	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs7295147	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs7966561	0.86[CHB][hapmap]
rs7968356	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7979029	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899213	chr12:66389968-66500036	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv832446	chr12:66393863-66501484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10878376	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10878376	TMBIM4	cis	uninvolved skin	skin_eQTL
rs10878376	TMBIM4	cis	lesional skin	skin_eQTL
rs10878376	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs10878376	RP11-745O10.2	cis	Thyroid	GTEx
rs10878376	RP11-745O10.2	cis	Whole Blood	GTEx
rs10878376	TMBIM4	cis	normal skin	skin_eQTL
rs10878376	RP11-745O10.2	cis	lung	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66468800-66486000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:66479600-66482200	Enhancers	HepG2	liver
3	chr12:66479800-66481000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:66480200-66480800	Weak transcription	HSMM	muscle
5	chr12:66480200-66481200	Enhancers	NHDF-Ad	bronchial
6	chr12:66480200-66481400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:66480400-66481000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:66480400-66481000	Enhancers	Osteobl	bone

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