Variant report

Variant	rs6731927
Chromosome Location	chr2:55735206-55735207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55734348..55736732-chr2:55747645..55749289,2	K562	blood:
2	chr2:55733547..55736199-chr2:55744050..55746817,2	MCF-7	breast:
3	chr2:55735103..55738045-chr2:55741187..55743259,2	K562	blood:

Variant related genes	Relation type
ENSG00000163001	Chromatin interaction

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

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

rs_ID	r²[population]
rs10184287	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs1037508	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10427222	0.81[JPT][hapmap]
rs1045910	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12463766	0.88[ASN][1000 genomes]
rs12617829	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs12619756	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12989898	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs13016772	0.85[ASN][1000 genomes]
rs13028892	1.00[CEU][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1373228	0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs1563201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814457	0.86[ASN][1000 genomes]
rs1975486	0.95[JPT][hapmap]
rs2168097	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2586946	0.93[ASN][1000 genomes]
rs2586948	0.93[ASN][1000 genomes]
rs2586949	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2586951	0.81[ASN][1000 genomes]
rs2586965	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2627758	0.94[ASN][1000 genomes]
rs2627763	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2627778	0.91[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs2627783	0.82[ASN][1000 genomes]
rs3748945	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs3816489	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4233962	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671248	1.00[CEU][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs61475257	0.94[ASN][1000 genomes]
rs62165178	0.84[ASN][1000 genomes]
rs6545503	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs6545505	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs706549	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs706550	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs706551	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs730884	0.82[ASN][1000 genomes]
rs744514	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7559307	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs7575973	0.82[AMR][1000 genomes]
rs7585484	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7605486	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7605504	0.94[ASN][1000 genomes]
rs782569	0.81[ASN][1000 genomes]
rs782574	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs782580	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs782583	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs782589	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs782591	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs782593	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs782597	0.88[ASN][1000 genomes]
rs782598	0.93[ASN][1000 genomes]
rs782603	0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs782612	0.94[ASN][1000 genomes]
rs782614	0.82[ASN][1000 genomes]
rs782620	0.91[CHB][hapmap]
rs782621	0.82[CHB][hapmap]
rs782628	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs782636	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs782647	0.83[ASN][1000 genomes]
rs782648	0.89[ASN][1000 genomes]
rs782651	0.89[ASN][1000 genomes]
rs9636439	0.95[JPT][hapmap];0.82[ASN][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
rs6731927	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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