Variant report

Variant	rs10861298
Chromosome Location	chr12:105358091-105358092
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	chr12:105354302..105359267-chr12:105378860..105381853,4	MCF-7	breast:
2	chr12:105351015..105355585-chr12:105357288..105360893,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151131	Chromatin interaction
ENSG00000136052	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10861283	0.85[ASN][1000 genomes]
rs10861284	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10861285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10861289	0.88[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs10861290	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10861299	0.85[CEU][hapmap]
rs11112211	0.89[JPT][hapmap]
rs11112213	0.89[JPT][hapmap]
rs11112214	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11112216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11112219	0.87[ASN][1000 genomes]
rs11112222	0.83[ASN][1000 genomes]
rs11112226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11112239	0.83[ASN][1000 genomes]
rs11112240	0.83[ASN][1000 genomes]
rs11112244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11112247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11112255	0.90[ASN][1000 genomes]
rs11112262	1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs11112263	0.85[CEU][hapmap]
rs11112267	0.90[ASN][1000 genomes]
rs11112272	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs11112273	0.95[ASN][1000 genomes]
rs11112278	0.95[ASN][1000 genomes]
rs11112280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11112281	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11112282	0.95[ASN][1000 genomes]
rs11112284	0.85[CEU][hapmap]
rs11112288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11112289	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11112300	0.95[ASN][1000 genomes]
rs11112301	0.95[ASN][1000 genomes]
rs11112302	0.95[ASN][1000 genomes]
rs11112305	0.95[ASN][1000 genomes]
rs11112312	0.95[ASN][1000 genomes]
rs11112317	0.95[ASN][1000 genomes]
rs11112344	1.00[JPT][hapmap]
rs1129593	0.80[CEU][hapmap]
rs11519610	0.95[ASN][1000 genomes]
rs11519721	0.95[ASN][1000 genomes]
rs12367133	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12368856	0.83[ASN][1000 genomes]
rs12371663	0.87[ASN][1000 genomes]
rs12372030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12372069	0.83[ASN][1000 genomes]
rs2047128	0.89[JPT][hapmap]
rs4318051	0.85[CEU][hapmap]
rs4405400	0.81[ASN][1000 genomes]
rs6539176	0.85[CEU][hapmap]
rs7303811	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7959207	0.85[EUR][1000 genomes]
rs7970173	0.83[CEU][hapmap]
rs9943769	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10861298	C12orf45	cis	cerebellum	SCAN
rs10861298	C12orf45	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105353800-105358800	Weak transcription	GM12878-XiMat	blood
2	chr12:105356600-105359400	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr12:105357000-105358800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:105357400-105358800	Enhancers	Fetal Brain Male	brain
5	chr12:105357400-105359000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:105357600-105358200	Enhancers	Fetal Brain Female	brain
7	chr12:105358000-105358200	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr12:105358000-105358400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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