Variant report

Variant	rs12423974
Chromosome Location	chr12:72662278-72662279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:72657850..72659523-chr12:72661531..72663362,2	K562	blood:
2	chr12:72410580..72411155-chr12:72661452..72662373,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12423531	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12424644	0.85[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12425628	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12426189	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12579464	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17110954	0.85[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17725193	0.82[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17725446	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17782464	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3803029	0.82[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4073007	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]
rs4073008	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4073009	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4408352	1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4523734	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4544048	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4616080	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56262673	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57557274	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58523622	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59211589	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59585902	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73336638	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73336641	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73336644	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73336682	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73336696	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73350816	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74103677	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74103702	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74105306	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960623	0.82[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7979378	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
5	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
6	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
7	nsv469465	chr12:72655925-73259114	Weak transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv559363	chr12:72655925-73259114	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12423974	DYRK2	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:72630400-72663200	Weak transcription	NH-A	brain
2	chr12:72646600-72663400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr12:72647600-72663000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:72647800-72663200	Weak transcription	Fetal Intestine Small	intestine
5	chr12:72648000-72663200	Weak transcription	NHLF	lung
6	chr12:72649600-72663400	Weak transcription	Pancreas	Pancrea
7	chr12:72651600-72663400	Weak transcription	Fetal Kidney	kidney
8	chr12:72656000-72663400	Weak transcription	Ovary	ovary
9	chr12:72661400-72663200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:72661600-72662600	Genic enhancers	HMEC	breast
11	chr12:72661600-72664800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:72661800-72665200	Active TSS	Adipose Nuclei	Adipose
13	chr12:72662000-72663400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:72662200-72662400	Enhancers	H9 Cell Line	embryonic stem cell
15	chr12:72662200-72662400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:72662200-72662400	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:72662200-72662400	Enhancers	Brain Angular Gyrus	brain
18	chr12:72662200-72662400	Flanking Active TSS	Fetal Intestine Large	intestine
19	chr12:72662200-72663000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:72662200-72664600	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr12:72662200-72664800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr12:72662200-72665200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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