Variant report

Variant	rs12463766
Chromosome Location	chr2:55743729-55743730
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	chr2:55659643..55661172-chr2:55741607..55744341,2	MCF-7	breast:
2	chr2:55741679..55743940-chr2:55745074..55747931,2	K562	blood:

Variant related genes	Relation type
ENSG00000163001	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1037508	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1045910	0.85[ASN][1000 genomes]
rs12619756	0.84[ASN][1000 genomes]
rs12989898	0.90[ASN][1000 genomes]
rs13016772	0.94[ASN][1000 genomes]
rs13028892	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1563201	0.88[ASN][1000 genomes]
rs2168097	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2586946	0.82[ASN][1000 genomes]
rs2586948	0.82[ASN][1000 genomes]
rs2586965	0.82[ASN][1000 genomes]
rs2627758	0.82[ASN][1000 genomes]
rs2627763	0.82[ASN][1000 genomes]
rs2627783	0.89[ASN][1000 genomes]
rs3748945	0.93[ASN][1000 genomes]
rs3816489	0.91[ASN][1000 genomes]
rs4233962	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671248	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671250	0.81[AFR][1000 genomes]
rs61475257	0.85[ASN][1000 genomes]
rs62165178	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545505	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545508	0.83[AFR][1000 genomes]
rs6731927	0.88[ASN][1000 genomes]
rs6736996	0.82[AFR][1000 genomes]
rs6760959	0.82[AFR][1000 genomes]
rs730884	0.90[ASN][1000 genomes]
rs744514	0.90[ASN][1000 genomes]
rs7571482	0.80[ASN][1000 genomes]
rs7574398	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7574409	0.81[AFR][1000 genomes]
rs7585484	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7605486	0.84[ASN][1000 genomes]
rs7605504	0.84[ASN][1000 genomes]
rs782589	0.81[ASN][1000 genomes]
rs782591	0.82[ASN][1000 genomes]
rs782593	0.82[ASN][1000 genomes]
rs782598	0.82[ASN][1000 genomes]
rs782603	0.81[ASN][1000 genomes]
rs782612	0.82[ASN][1000 genomes]
rs9636439	0.89[ASN][1000 genomes]
rs9808054	0.82[AFR][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	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
6	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12463766	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55739000-55745600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:55739000-55745800	Weak transcription	Brain Angular Gyrus	brain
3	chr2:55739000-55745800	Weak transcription	Thymus	Thymus
4	chr2:55739000-55745800	Weak transcription	NHEK	skin
5	chr2:55741800-55745800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:55743400-55744600	Enhancers	Fetal Brain Male	brain

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