Variant report

Variant	rs4073007
Chromosome Location	chr12:72648077-72648078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZFC3H1-6	chr12:72647288-72652020	ENSG00000236333
2	lnc-ZFC3H1-6	chr12:72647293-72649554	ENSG00000236333
3	lnc-ZFC3H1-6	chr12:72647334-72648394	XLOC_010128
4	lnc-ZFC3H1-6	chr12:72647293-72649554	XLOC_010128
5	lnc-ZFC3H1-6	chr12:72647497-72648394	XLOC_010128

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10784960	0.85[JPT][hapmap]
rs10879394	0.85[JPT][hapmap]
rs12423531	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12423974	0.82[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12424644	0.85[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12425628	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12426189	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12579464	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17110954	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17725193	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17725446	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17782464	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3803029	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4073008	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4073009	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4237861	0.85[JPT][hapmap]
rs4408352	0.82[JPT][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4523734	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4544048	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4584622	0.85[JPT][hapmap]
rs4616080	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56262673	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57557274	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58523622	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59211589	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59585902	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7295741	0.85[JPT][hapmap]
rs73336638	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73336641	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73336644	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73336682	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73336696	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73350816	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74103677	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74103702	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74105306	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7960623	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7979378	0.88[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422452	chr12:72485933-73175581	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv899257	chr12:72569746-73145896	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv832452	chr12:72584971-72764495	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv770	chr12:72615837-72660510	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv899258	chr12:72624088-72957899	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv559362	chr12:72641784-72694691	Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv1044083	chr12:72647640-73275526	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4073007	DYRK2	cis	parietal	SCAN
rs4073007	TRHDE	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:72630400-72663200	Weak transcription	NH-A	brain
2	chr12:72645200-72649000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:72646200-72650200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:72646400-72649000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:72646600-72663400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr12:72647400-72648600	Strong transcription	Adipose Nuclei	Adipose
7	chr12:72647600-72663000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:72647800-72648400	Strong transcription	HMEC	breast
9	chr12:72647800-72649400	Strong transcription	Fetal Intestine Large	intestine
10	chr12:72647800-72663200	Weak transcription	Fetal Intestine Small	intestine
11	chr12:72648000-72649800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:72648000-72663200	Weak transcription	NHLF	lung

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