Variant report

Variant	rs12907442
Chromosome Location	chr15:40968386-40968387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10518697	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070283	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11630273	0.83[EUR][1000 genomes]
rs11633184	0.81[EUR][1000 genomes]
rs12148915	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12324748	0.81[EUR][1000 genomes]
rs12385982	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12441754	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12442560	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12591044	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12592524	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12903817	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908316	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913739	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12915636	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17674454	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17747423	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17747633	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1801321	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1814541	0.83[EUR][1000 genomes]
rs2412525	0.80[EUR][1000 genomes]
rs2619682	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28529389	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28866515	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28891195	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34305357	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34739056	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34824658	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35127391	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35684277	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35842610	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4923880	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924486	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924492	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924496	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4924498	0.84[AMR][1000 genomes]
rs4924502	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5030789	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56409425	0.81[AMR][1000 genomes]
rs59244061	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62019876	0.81[EUR][1000 genomes]
rs62019879	0.83[EUR][1000 genomes]
rs71471880	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165509	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175747	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176245	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7176590	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7177265	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7180135	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7182499	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8029530	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036891	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037180	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038122	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042386	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957603	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9920676	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[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	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv529030	chr15:40956471-41012695	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv904100	chr15:40959624-40994706	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs12907442	CCDC32	cis	multi-tissue	Pritchard
rs12907442	C15orf57	cis	Muscle Skeletal	GTEx
rs12907442	C15orf57	cis	Nerve Tibial	GTEx
rs12907442	RAD51	cis	multi-tissue	Pritchard
rs12907442	RP11-111A22.1	cis	lung	GTEx
rs12907442	C15orf57	cis	Artery Tibial	GTEx
rs12907442	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs12907442	C15orf57	cis	Artery Aorta	GTEx
rs12907442	C15orf57	cis	Stomach	GTEx
rs12907442	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12907442	C15orf57	cis	Esophagus Muscularis	GTEx
rs12907442	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs12907442	C15orf57	cis	lung	GTEx
rs12907442	C15orf57	cis	Esophagus Mucosa	GTEx
rs12907442	C15orf57	cis	Heart Left Ventricle	GTEx
rs12907442	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs12907442	RP11-111A22.1	cis	Artery Tibial	GTEx
rs12907442	CCDC32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40913800-40986000	Weak transcription	A549	lung
2	chr15:40943000-40971400	Weak transcription	Primary B cells from cord blood	blood
3	chr15:40945000-40984200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:40950000-40981200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:40955200-40976600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:40955200-40983200	Weak transcription	Fetal Intestine Small	intestine
7	chr15:40955800-40976000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:40956800-40971200	Weak transcription	Dnd41	blood
9	chr15:40958600-40981000	Weak transcription	Thymus	Thymus
10	chr15:40960400-40977000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:40968000-40968400	Enhancers	HepG2	liver

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