Variant report

Variant	rs2468397
Chromosome Location	chr12:105334343-105334344
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	chr12:105333400..105336266-chr12:105343933..105346913,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136052	Chromatin interaction
ENSG00000265054	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10507183	0.88[CHB][hapmap];0.90[CHD][hapmap];0.90[ASN][1000 genomes]
rs10507185	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10778354	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10778356	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10861278	0.89[ASN][1000 genomes]
rs10861280	0.86[ASN][1000 genomes]
rs10861282	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10861291	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10861293	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10861295	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10861297	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112208	0.88[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs11112221	0.89[ASN][1000 genomes]
rs11112234	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12230637	0.88[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs17829927	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2047126	0.88[ASN][1000 genomes]
rs2245695	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2249941	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2252843	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2264883	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2264893	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2453163	0.90[ASN][1000 genomes]
rs2453164	0.90[ASN][1000 genomes]
rs2453169	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs2463430	0.85[ASN][1000 genomes]
rs2468088	0.84[ASN][1000 genomes]
rs2468094	0.86[ASN][1000 genomes]
rs2468096	0.89[ASN][1000 genomes]
rs2468098	0.89[ASN][1000 genomes]
rs2468103	0.90[ASN][1000 genomes]
rs2468107	0.88[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2468108	0.90[ASN][1000 genomes]
rs2468336	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2468338	0.88[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs2468339	0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2468341	0.88[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs2468342	0.86[ASN][1000 genomes]
rs2468343	0.88[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[ASN][1000 genomes]
rs2468344	0.84[ASN][1000 genomes]
rs2468345	0.86[ASN][1000 genomes]
rs2468396	0.95[EUR][1000 genomes]
rs2642119	0.90[ASN][1000 genomes]
rs2642120	0.94[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2730294	0.88[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs3890816	0.83[CEU][hapmap]
rs4130161	0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4257060	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4537841	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4630370	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4644704	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4964116	0.88[CEU][hapmap]
rs57987047	0.82[EUR][1000 genomes]
rs7959777	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7961766	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7971260	0.90[ASN][1000 genomes]
rs7971392	0.91[ASN][1000 genomes]
rs9705471	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[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
rs2468397	GNPTAB	cis	parietal	SCAN
rs2468397	C12orf42	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105323600-105338000	Weak transcription	Pancreas	Pancrea
2	chr12:105332400-105334800	Enhancers	Liver	Liver
3	chr12:105332400-105336000	Weak transcription	Aorta	Aorta
4	chr12:105332400-105342400	Weak transcription	Gastric	stomach
5	chr12:105333200-105346200	Weak transcription	HepG2	liver
6	chr12:105333400-105334800	Weak transcription	Adipose Nuclei	Adipose
7	chr12:105333400-105334800	Weak transcription	Stomach Mucosa	stomach
8	chr12:105333400-105335000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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