Variant report

Variant	rs28809230
Chromosome Location	chr12:123865361-123865362
allele	C/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	chr12:123574636..123576162-chr12:123864283..123866660,2	K562	blood:
3	chr12:123846590..123852305-chr12:123861449..123873718,39	K562	blood:

Variant related genes	Relation type
ENSG00000256092	Chromatin interaction
ENSG00000139697	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11830103	0.83[EUR][1000 genomes]
rs12298826	0.82[EUR][1000 genomes]
rs12299125	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12316131	0.82[EUR][1000 genomes]
rs12322888	0.83[EUR][1000 genomes]
rs28372579	0.91[EUR][1000 genomes]
rs28406193	0.89[EUR][1000 genomes]
rs28413626	0.92[EUR][1000 genomes]
rs28458312	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28472704	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28576953	0.89[EUR][1000 genomes]
rs28582096	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28583837	0.97[EUR][1000 genomes]
rs28592876	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28636834	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28675824	0.93[EUR][1000 genomes]
rs28683528	0.91[EUR][1000 genomes]
rs28855757	0.87[EUR][1000 genomes]
rs34997336	0.82[EUR][1000 genomes]
rs67624109	0.83[EUR][1000 genomes]
rs7485502	0.89[EUR][1000 genomes]
rs7980687	0.83[EUR][1000 genomes]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs28809230	CDK2AP1	cis	Adipose Subcutaneous	GTEx
rs28809230	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs28809230	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs28809230	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs28809230	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs28809230	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs28809230	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs28809230	RP11-282O18.3	cis	Adipose Subcutaneous	GTEx
rs28809230	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 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	chr12:123861400-123866800	Weak transcription	K562	blood
5	chr12:123864000-123866800	Weak transcription	HepG2	liver
6	chr12:123864000-123867200	Weak transcription	Placenta	Placenta
7	chr12:123864200-123867200	Weak transcription	A549	lung
8	chr12:123864200-123867400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:123864400-123867000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:123864400-123867200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:123864400-123867800	Weak transcription	HMEC	breast
12	chr12:123864400-123867800	Weak transcription	NHEK	skin
13	chr12:123864600-123868000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links