Variant report

Variant	rs28675824
Chromosome Location	chr12:123853449-123853450
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123846452..123851332-chr12:123852083..123855432,7	K562	blood:
2	chr12:123852496..123855260-chr12:123856504..123859188,2	K562	blood:
3	chr12:123845329..123854937-chr12:123865496..123876607,58	K562	blood:
4	chr12:123852265..123854737-chr12:124067647..124070579,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183955	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000247373	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1060105	0.84[EUR][1000 genomes]
rs10773008	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10846515	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11057270	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11830103	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12298826	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12299125	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12304248	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12316131	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12322888	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28372579	0.89[EUR][1000 genomes]
rs28406193	0.88[EUR][1000 genomes]
rs28413626	0.91[EUR][1000 genomes]
rs28458312	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28472704	0.88[EUR][1000 genomes]
rs28576953	0.88[EUR][1000 genomes]
rs28582096	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28583837	0.96[EUR][1000 genomes]
rs28592876	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28636834	0.94[EUR][1000 genomes]
rs28683528	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28809230	0.93[EUR][1000 genomes]
rs28855757	0.85[EUR][1000 genomes]
rs34997336	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4759420	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs67624109	0.87[EUR][1000 genomes]
rs7485502	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7955457	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7980687	0.87[EUR][1000 genomes]
rs9300255	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs28675824	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs28675824	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs28675824	RP11-282O18.3	cis	Adipose Subcutaneous	GTEx
rs28675824	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs28675824	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs28675824	CDK2AP1	cis	Adipose Subcutaneous	GTEx
rs28675824	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs28675824	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs28675824	LOC283378	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123850400-123856200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:123850600-123867200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:123850600-123867800	Weak transcription	Right Atrium	heart
4	chr12:123850800-123856800	Weak transcription	HepG2	liver
5	chr12:123851200-123856200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr12:123852600-123856000	Weak transcription	A549	lung
7	chr12:123853400-123854800	Enhancers	GM12878-XiMat	blood
8	chr12:123853400-123854800	Enhancers	K562	blood

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