Variant report

Variant	rs4672052
Chromosome Location	chr2:55732018-55732019
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55731157..55733900-chr2:55736800..55738554,2	MCF-7	breast:
2	chr2:55719796..55722184-chr2:55731465..55733382,2	MCF-7	breast:
3	chr2:55726280..55728850-chr2:55731449..55734016,2	K562	blood:

Variant related genes	Relation type
ENSG00000239189	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10165864	0.84[EUR][1000 genomes]
rs10181648	0.85[EUR][1000 genomes]
rs10454749	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10460508	0.91[CEU][hapmap]
rs10496050	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1058582	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1084522	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11125579	0.95[EUR][1000 genomes]
rs11125581	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17278044	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17369191	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17798852	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1823893	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1975484	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1975487	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2586947	0.80[EUR][1000 genomes]
rs2586954	0.91[CEU][hapmap]
rs2586969	0.87[CEU][hapmap]
rs2586970	0.87[CEU][hapmap]
rs2627759	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2627765	0.83[CEU][hapmap]
rs2627776	0.91[CEU][hapmap]
rs35504023	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3762513	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4290693	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4672054	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4672055	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4672056	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55761024	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58003472	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62165168	0.82[EUR][1000 genomes]
rs62165173	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62165181	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62165182	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62165183	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62165184	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62165196	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62165197	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6545506	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6739513	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs706548	0.83[CEU][hapmap]
rs7582278	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7594279	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7598650	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs782568	0.91[CEU][hapmap]
rs782586	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs782587	0.82[EUR][1000 genomes]
rs782588	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs782590	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs782594	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs782595	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs782599	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs782600	0.80[EUR][1000 genomes]
rs782601	0.80[EUR][1000 genomes]
rs782602	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs782606	0.91[CEU][hapmap]
rs782630	0.80[CEU][hapmap]
rs782649	0.82[EUR][1000 genomes]
rs782650	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs782652	0.91[CEU][hapmap]
rs935177	0.87[CEU][hapmap]
rs9917139	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv521318	chr2:55716650-55736704	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	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
rs4672052	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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