Variant report

Variant	rs483499
Chromosome Location	chr12:10120913-10120914
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:10120681-10121248	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
CLEC12A	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs2760953	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2922161	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2922162	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2961542	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2984956	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs477751	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs478829	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs479624	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs483576	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs525013	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs526157	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56060582	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs562627	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs562839	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs611819	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs611821	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs612227	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs612270	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs613123	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs640817	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs643003	0.85[EUR][1000 genomes]
rs7137254	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7953702	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7953814	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044587	chr12:10029514-10123414	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv523050	chr12:10031880-10124373	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv898755	chr12:10069302-10186284	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs483499	CLEC12A	cis	Whole Blood	GTEx
rs483499	CLEC12B	cis	Whole Blood	GTEx
rs483499	CLEC12A	cis	Muscle Skeletal	GTEx
rs483499	RP11-133L14.5	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10117800-10122000	Active TSS	Monocytes-CD14+_RO01746	blood
2	chr12:10120200-10121000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
3	chr12:10120200-10125400	Enhancers	Primary neutrophils fromperipheralblood	blood

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