Variant report

Variant	rs11130185
Chromosome Location	chr3:49249871-49249872
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11130184	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11715581	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11716334	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11717524	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11920267	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12490393	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12629637	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12629759	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12631989	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12637576	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13064780	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2117938	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2334958	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35174559	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35218722	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4308307	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4367098	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4499638	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4536858	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4955418	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4955419	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4955432	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55713230	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57245267	0.80[AFR][1000 genomes]
rs6794924	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6795756	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7638154	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7652746	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs11130185	WDR6	cis	Artery Tibial	GTEx
rs11130185	NICN1	cis	Thyroid	GTEx
rs11130185	WDR6	cis	Esophagus Muscularis	GTEx
rs11130185	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs11130185	AMT	cis	Whole Blood	GTEx
rs11130185	AMT	cis	Artery Aorta	GTEx
rs11130185	WDR6	cis	Nerve Tibial	GTEx
rs11130185	CCDC36	cis	Artery Tibial	GTEx
rs11130185	CCDC36	cis	Esophagus Muscularis	GTEx
rs11130185	WDR6	cis	Muscle Skeletal	GTEx
rs11130185	AMT	cis	Thyroid	GTEx
rs11130185	WDR6	cis	Adipose Subcutaneous	GTEx
rs11130185	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs11130185	WDR6	cis	Whole Blood	GTEx
rs11130185	NICN1-AS1	cis	Thyroid	GTEx
rs11130185	WDR6	cis	lung	GTEx
rs11130185	WDR6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49237600-49255600	Weak transcription	Left Ventricle	heart
2	chr3:49237800-49251000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:49237800-49251200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:49238200-49251000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:49238200-49251000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:49238200-49251000	Weak transcription	NHLF	lung
7	chr3:49238200-49255400	Weak transcription	Right Ventricle	heart
8	chr3:49239400-49251000	Weak transcription	Ovary	ovary
9	chr3:49243200-49255200	Weak transcription	Fetal Heart	heart
10	chr3:49243400-49251200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:49245800-49255200	Weak transcription	Right Atrium	heart
12	chr3:49246200-49250000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:49246400-49251200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:49246800-49255200	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:49247000-49251200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:49247400-49255400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:49248600-49250200	Strong transcription	Osteobl	bone
18	chr3:49249200-49251000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:49249200-49255400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:49249400-49251600	Weak transcription	Fetal Lung	lung
21	chr3:49249600-49250600	Strong transcription	Fetal Muscle Leg	muscle
22	chr3:49249800-49250200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:49249800-49251200	Strong transcription	Adipose Nuclei	Adipose
24	chr3:49249800-49251800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:49249800-49251800	ZNF genes & repeats	Fetal Stomach	stomach

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