Variant report

Variant	rs717179
Chromosome Location	chr12:9395908-9395909
allele	A/G
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	GATA3	chr12:9395658-9395976	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9389499..9391072-chr12:9394393..9395954,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256427	TF binding region
PTMAP4	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10771440	0.90[ASN][1000 genomes]
rs10771443	0.90[ASN][1000 genomes]
rs10771445	0.85[ASN][1000 genomes]
rs10843242	0.87[ASN][1000 genomes]
rs10843243	0.87[ASN][1000 genomes]
rs10843244	0.87[ASN][1000 genomes]
rs11049800	0.87[ASN][1000 genomes]
rs11049844	0.83[ASN][1000 genomes]
rs12579180	0.91[ASN][1000 genomes]
rs187536	0.87[ASN][1000 genomes]
rs194037	0.87[ASN][1000 genomes]
rs2059760	0.89[ASN][1000 genomes]
rs2059761	0.89[ASN][1000 genomes]
rs2288363	0.85[ASN][1000 genomes]
rs252027	0.87[ASN][1000 genomes]
rs252028	0.87[ASN][1000 genomes]
rs252029	0.87[ASN][1000 genomes]
rs252030	0.87[ASN][1000 genomes]
rs252032	0.87[ASN][1000 genomes]
rs252033	0.87[ASN][1000 genomes]
rs34332	0.89[ASN][1000 genomes]
rs34333	0.88[ASN][1000 genomes]
rs34334	0.89[ASN][1000 genomes]
rs34371	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34372	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4883225	0.89[ASN][1000 genomes]
rs4883226	0.86[ASN][1000 genomes]
rs61916190	0.81[ASN][1000 genomes]
rs717181	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299846	0.90[ASN][1000 genomes]
rs7309684	0.91[ASN][1000 genomes]
rs7958291	0.90[ASN][1000 genomes]
rs7967738	0.87[ASN][1000 genomes]
rs7974378	0.89[ASN][1000 genomes]
rs7976100	0.90[ASN][1000 genomes]
rs7980226	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980256	0.87[ASN][1000 genomes]
rs877169	0.94[ASN][1000 genomes]
rs968786	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv527404	chr12:9250601-9435244	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv523958	chr12:9303440-9549072	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv557355	chr12:9309995-9529015	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1035953	chr12:9314481-9544655	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
7	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
8	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
10	nsv1048917	chr12:9393282-9436132	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs717179	DDX12P	cis	Muscle Skeletal	GTEx
rs717179	DDX12P	cis	Nerve Tibial	GTEx
rs717179	RP11-22B23.1	cis	lung	GTEx
rs717179	DDX12P	cis	Thyroid	GTEx
rs717179	RP11-22B23.1	cis	Muscle Skeletal	GTEx
rs717179	DDX12P	cis	Artery Tibial	GTEx
rs717179	A2MP1	cis	Adipose Subcutaneous	GTEx
rs717179	RP11-22B23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs717179	RP11-22B23.1	cis	Artery Tibial	GTEx
rs717179	A2MP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9393200-9396800	Weak transcription	Psoas Muscle	Psoas
2	chr12:9393200-9397400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:9393200-9397400	Weak transcription	Pancreas	Pancrea
4	chr12:9393200-9397400	Weak transcription	Right Ventricle	heart
5	chr12:9393400-9397400	Weak transcription	HMEC	breast
6	chr12:9393400-9398200	Enhancers	HepG2	liver
7	chr12:9393600-9408200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr12:9393600-9411400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:9394200-9397200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr12:9394200-9397800	Enhancers	Brain Hippocampus Middle	brain
11	chr12:9394400-9396400	Weak transcription	Liver	Liver
12	chr12:9394600-9396800	Weak transcription	Fetal Lung	lung
13	chr12:9394800-9396000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:9395000-9397400	Weak transcription	Brain Angular Gyrus	brain
15	chr12:9395200-9407800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:9395400-9396800	Weak transcription	Brain Anterior Caudate	brain
17	chr12:9395800-9396000	Enhancers	Brain Cingulate Gyrus	brain
18	chr12:9395800-9396800	Enhancers	Brain Substantia Nigra	brain
19	chr12:9395800-9398000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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