Variant report

Variant	rs10506442
Chromosome Location	chr12:62851547-62851548
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62849898..62851634-chr12:62858993..62861083,2	K562	blood:
2	chr12:62850480..62852010-chr12:62854523..62856812,2	MCF-7	breast:
3	chr12:62842612..62845567-chr12:62849040..62853936,4	K562	blood:

Variant related genes	Relation type
ENSG00000061987	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10506443	0.88[JPT][hapmap];0.90[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12146793	0.89[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12423344	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12424006	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12427111	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13328991	1.00[CEU][hapmap]
rs1532394	1.00[CEU][hapmap]
rs17097966	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17098038	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17098087	1.00[CEU][hapmap]
rs17098096	1.00[CEU][hapmap]
rs17098098	1.00[CEU][hapmap]
rs17120341	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1982991	0.89[JPT][hapmap]
rs4763172	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4763173	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4763176	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57715507	0.83[EUR][1000 genomes]
rs59191400	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61556144	0.83[EUR][1000 genomes]
rs61919478	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61919479	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61919485	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61921903	0.88[ASN][1000 genomes]
rs61921904	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61921905	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61921908	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61921909	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs61921910	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61921911	0.82[EUR][1000 genomes]
rs61921913	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61921914	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7136696	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7307786	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7309338	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7316437	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73323255	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7958721	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7964791	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7965328	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7969992	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv899158	chr12:62783967-62937259	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv899159	chr12:62783967-62945245	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10506442	METTL1	cis	cerebellum	SCAN
rs10506442	MON2	cis	cerebellum	SCAN
rs10506442	MARS	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62851200-62852000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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