Variant report

Variant	rs2640562
Chromosome Location	chr12:56466473-56466474
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56464666..56467549-chr12:56498079..56499620,2	MCF-7	breast:
2	chr12:56460906..56463443-chr12:56465823..56468206,2	K562	blood:

Variant related genes	Relation type
ENSG00000170515	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10876866	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10876870	0.85[ASN][1000 genomes]
rs11171739	0.86[ASN][1000 genomes]
rs1689510	0.84[EUR][1000 genomes]
rs1701704	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1702877	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2017445	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2271194	0.90[ASN][1000 genomes]
rs2292239	0.88[EUR][1000 genomes]
rs2456973	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2640564	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34415530	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3741499	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4759229	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61938962	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61938963	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs705696	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs705704	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs705705	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7297175	0.86[ASN][1000 genomes]
rs7302200	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7312770	0.91[ASN][1000 genomes]
rs772921	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7971751	0.85[ASN][1000 genomes]
rs877636	0.88[EUR][1000 genomes];0.90[ASN][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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription 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 target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2640562	DEFB124	trans	lymphoblastoid	RTeQTL
rs2640562	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs2640562	AC034102.1	cis	Muscle Skeletal	GTEx
rs2640562	RAB5B	cis	Muscle Skeletal	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56437000-56472800	Weak transcription	Right Atrium	heart
2	chr12:56454400-56467800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:56464800-56467200	Enhancers	Placenta	Placenta
4	chr12:56465000-56466600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:56465400-56466600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:56465400-56467000	Enhancers	HepG2	liver
7	chr12:56465800-56467000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr12:56466200-56472400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:56466400-56467400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:56466400-56467400	Weak transcription	NHEK	skin
11	chr12:56466400-56471800	Weak transcription	Hela-S3	cervix
12	chr12:56466400-56472600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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