Variant report

Variant	rs12022421
Chromosome Location	chr1:85523398-85523399
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85521255..85524201-chr1:85525126..85527419,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10782534	1.00[CEU][hapmap];0.91[GIH][hapmap]
rs10782536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10873672	1.00[CEU][hapmap];0.91[GIH][hapmap]
rs10873676	0.81[EUR][1000 genomes]
rs10873678	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10873679	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10873682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10873683	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161497	1.00[CEU][hapmap]
rs11161498	1.00[CEU][hapmap]
rs11161502	0.81[EUR][1000 genomes]
rs11161513	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161514	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161525	0.80[CHB][hapmap]
rs11161526	0.81[CHB][hapmap]
rs12030990	0.81[CHB][hapmap]
rs12062414	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12063120	0.81[CHB][hapmap]
rs12130357	1.00[CEU][hapmap]
rs12138711	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2486755	1.00[CEU][hapmap]
rs3850430	0.80[EUR][1000 genomes]
rs3895846	0.80[EUR][1000 genomes]
rs486751	1.00[CEU][hapmap]
rs4907123	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4907125	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs531423	1.00[CEU][hapmap]
rs589653	1.00[CEU][hapmap]
rs600536	1.00[CEU][hapmap]
rs603746	1.00[CEU][hapmap]
rs625045	1.00[CEU][hapmap];0.86[GIH][hapmap]
rs632545	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs651916	1.00[CEU][hapmap]
rs6576736	1.00[CEU][hapmap];0.91[GIH][hapmap]
rs6677091	1.00[CEU][hapmap]
rs668860	1.00[CEU][hapmap];0.91[GIH][hapmap]
rs6691970	1.00[CEU][hapmap];0.91[GIH][hapmap]
rs6700622	1.00[CEU][hapmap]
rs677476	1.00[CEU][hapmap]
rs7516625	1.00[CEU][hapmap]
rs7522851	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs7534574	0.81[CHB][hapmap]
rs7541684	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12022421	MCOLN3	cis	lymphoblastoid	seeQTL
rs12022421	LMO4	cis	cerebellum	SCAN
rs12022421	MCOLN2	cis	Adipose Subcutaneous	GTEx
rs12022421	MCOLN2	cis	multi-tissue	Pritchard
rs12022421	MCOLN2	cis	Thyroid	GTEx
rs12022421	MCOLN2	cis	lymphoblastoid	seeQTL
rs12022421	MCOLN2	cis	parietal	SCAN
rs12022421	MCOLN2	cis	Artery Tibial	GTEx
rs12022421	MCOLN3	cis	Thyroid	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85514800-85527400	Weak transcription	Aorta	Aorta
2	chr1:85515800-85523400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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