Variant report

Variant	rs28458312
Chromosome Location	chr12:123863265-123863266
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123847741..123850160-chr12:123863172..123865699,2	MCF-7	breast:
2	chr12:123846590..123852305-chr12:123861449..123873718,39	K562	blood:
3	chr12:123862454..123865045-chr12:123865570..123867094,2	K562	blood:

Variant related genes	Relation type
ENSG00000139697	Chromatin interaction
ENSG00000256092	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1060105	0.94[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs10772998	0.89[CEU][hapmap]
rs10773002	0.81[GIH][hapmap]
rs10773008	0.81[EUR][1000 genomes]
rs10846486	0.94[CEU][hapmap]
rs10846515	0.81[EUR][1000 genomes]
rs11057192	0.89[CEU][hapmap];0.97[TSI][hapmap]
rs11057270	0.82[EUR][1000 genomes]
rs11830103	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs12298826	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs12299125	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12304248	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs12316131	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs12322888	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[EUR][1000 genomes]
rs12817892	0.91[CEU][hapmap]
rs1402274	0.94[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap]
rs1402275	0.93[GIH][hapmap]
rs1533703	0.88[CEU][hapmap]
rs1568427	0.85[GIH][hapmap]
rs1609520	0.85[GIH][hapmap]
rs1716157	0.94[CEU][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap]
rs1716160	0.94[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs1716164	0.94[CEU][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap]
rs1716170	0.94[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs1716171	0.94[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs1727306	0.94[CEU][hapmap]
rs1727320	0.94[CEU][hapmap]
rs1727323	0.94[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs1727324	0.94[CEU][hapmap]
rs1727325	0.94[CEU][hapmap]
rs1727331	0.85[GIH][hapmap]
rs1727334	0.86[CEU][hapmap]
rs1790095	0.94[CEU][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap]
rs1790131	0.94[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs1879380	0.94[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs1969354	0.89[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs1980252	0.89[CEU][hapmap]
rs2337934	0.89[CEU][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap]
rs2682434	0.94[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs2695478	0.94[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs28372579	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28406193	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes]
rs28413626	0.95[EUR][1000 genomes]
rs28472704	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2851447	0.82[CEU][hapmap]
rs28569885	0.94[GIH][hapmap];0.91[TSI][hapmap]
rs28576953	0.92[EUR][1000 genomes]
rs28582096	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28583837	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28592876	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28625019	0.82[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes]
rs28636834	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28675824	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28676499	0.80[EUR][1000 genomes]
rs28683528	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28706696	0.82[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes]
rs28715490	0.81[EUR][1000 genomes]
rs28809230	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28855757	0.89[EUR][1000 genomes]
rs34997336	0.84[EUR][1000 genomes]
rs4372492	0.94[CEU][hapmap]
rs4460848	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs4759371	0.89[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs4759409	0.89[CEU][hapmap]
rs4759415	0.89[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs4759420	0.81[EUR][1000 genomes]
rs4930718	0.91[GIH][hapmap];0.88[TSI][hapmap]
rs4930719	0.80[EUR][1000 genomes]
rs6488868	0.88[ASW][hapmap]
rs67624109	0.86[EUR][1000 genomes]
rs7304782	0.85[GIH][hapmap]
rs7313483	0.89[CEU][hapmap]
rs7485502	0.92[EUR][1000 genomes]
rs7953929	0.94[CEU][hapmap];0.93[GIH][hapmap]
rs7955457	0.82[EUR][1000 genomes]
rs7980687	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs9300255	0.80[EUR][1000 genomes]
rs941305	0.94[CEU][hapmap]
rs941306	0.94[CEU][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	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv899579	chr12:123843017-123901480	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv826534	chr12:123859610-123876354	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs28458312	ANAPC5	cis	parietal	SCAN
rs28458312	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs28458312	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs28458312	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs28458312	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs28458312	CDK2AP1	cis	Adipose Subcutaneous	GTEx
rs28458312	CDK2AP1	cis	lymphoblastoid	seeQTL
rs28458312	PITPNM2	cis	cerebellum	SCAN
rs28458312	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs28458312	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs28458312	RP11-282O18.3	cis	Adipose Subcutaneous	GTEx
rs28458312	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123850600-123867200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:123850600-123867800	Weak transcription	Right Atrium	heart
3	chr12:123859200-123867200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:123859600-123863400	Weak transcription	A549	lung
5	chr12:123859600-123863400	Weak transcription	HepG2	liver
6	chr12:123861400-123866800	Weak transcription	K562	blood
7	chr12:123863200-123864600	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links