Variant report

Variant	rs11125579
Chromosome Location	chr2:55739804-55739805
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	chr2:55495971..55497708-chr2:55737888..55740106,2	MCF-7	breast:
2	chr2:55738996..55741436-chr2:55745150..55747793,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163001	Chromatin interaction
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10165864	0.86[EUR][1000 genomes]
rs10181648	0.87[EUR][1000 genomes]
rs10454749	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10496050	0.86[EUR][1000 genomes]
rs1058582	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1084522	0.83[EUR][1000 genomes]
rs11125581	0.86[EUR][1000 genomes]
rs17278044	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17369191	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17798852	0.86[EUR][1000 genomes]
rs1823893	0.87[EUR][1000 genomes]
rs1975484	0.85[EUR][1000 genomes]
rs2627759	0.82[EUR][1000 genomes]
rs35504023	0.86[EUR][1000 genomes]
rs3762513	0.90[EUR][1000 genomes]
rs4290693	0.86[EUR][1000 genomes]
rs4322879	0.82[AFR][1000 genomes]
rs4672052	0.95[EUR][1000 genomes]
rs4672054	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4672055	0.87[EUR][1000 genomes]
rs4672056	0.84[EUR][1000 genomes]
rs55761024	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58003472	0.87[EUR][1000 genomes]
rs62165173	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62165181	0.87[EUR][1000 genomes]
rs62165182	0.84[EUR][1000 genomes]
rs62165183	0.83[EUR][1000 genomes]
rs62165184	0.87[EUR][1000 genomes]
rs62165196	0.86[EUR][1000 genomes]
rs62165197	0.83[EUR][1000 genomes]
rs6545506	0.87[EUR][1000 genomes]
rs6739513	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7582278	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7594279	0.86[EUR][1000 genomes]
rs7598650	0.81[EUR][1000 genomes]
rs782586	0.82[EUR][1000 genomes]
rs782587	0.80[EUR][1000 genomes]
rs782588	0.83[EUR][1000 genomes]
rs782590	0.82[EUR][1000 genomes]
rs782594	0.83[EUR][1000 genomes]
rs782595	0.82[EUR][1000 genomes]
rs9917139	0.86[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	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11125579	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55739000-55741200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:55739000-55745600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:55739000-55745800	Weak transcription	Brain Angular Gyrus	brain
4	chr2:55739000-55745800	Weak transcription	Thymus	Thymus
5	chr2:55739000-55745800	Weak transcription	NHEK	skin

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