Variant report

Variant	rs12426100
Chromosome Location	chr12:21582633-21582634
allele	A/G
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: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1024734	0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10437776	0.83[MEX][hapmap];0.86[MKK][hapmap]
rs11046040	1.00[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]
rs12423173	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]
rs12423381	0.82[ASW][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12423536	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12817513	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.84[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	0.93[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	0.83[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	0.80[CHB][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7310391	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7314131	0.81[CHB][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs738027	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7957415	0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7959893	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7971245	0.87[CHB][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7973116	0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7974817	0.87[CHB][hapmap];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	0.81[AFR][1000 genomes];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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12426100	RECQL	cis	cerebellum	SCAN
rs12426100	PYROXD1	cis	parietal	SCAN
rs12426100	PYROXD1	cis	lymphoblastoid	seeQTL
rs12426100	LOC642732	trans	multi-tissue	Pritchard
rs12426100	PYROXD1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21581800-21590000	Weak transcription	HUVEC	blood vessel

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