Variant report

Variant	rs12423173
Chromosome Location	chr12:21581982-21581983
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	chr12:21581278..21584655-chr12:21586014..21590785,5	K562	blood:

Variant related genes	Relation type
ENSG00000121350	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1024734	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11046040	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11046044	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11835956	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12423381	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12423536	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424852	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426100	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426103	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12817513	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1860948	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2110164	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2417987	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs36142627	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4539382	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4762826	0.83[ASN][1000 genomes]
rs7131809	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7133131	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7133853	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7138089	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7298136	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7310391	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7314131	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs738027	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7957415	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7959893	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7971245	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7973116	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7974817	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9788265	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9788266	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519603	chr12:21526472-21584709	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv898894	chr12:21545532-21583242	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv526789	chr12:21555691-21590788	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv898895	chr12:21561645-21621891	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
5	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv469163	chr12:21579080-21592357	Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
9	nsv557742	chr12:21579080-21592357	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12423173	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs12423173	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs12423173	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs12423173	LOC642732	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21580400-21582000	Enhancers	Muscle Satellite Cultured Cells	--
2	chr12:21581800-21582000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:21581800-21590000	Weak transcription	HUVEC	blood vessel

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