Variant report

Variant	rs12637346
Chromosome Location	chr3:49284513-49284514
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49282535..49284630-chr3:49284779..49287492,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10154992	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11130183	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130186	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11130187	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11710434	0.83[AMR][1000 genomes]
rs11720542	0.83[AMR][1000 genomes]
rs2082923	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2099526	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4384984	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4955414	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4955417	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4955421	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4955423	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4955427	0.88[EUR][1000 genomes]
rs4955430	0.83[AMR][1000 genomes]
rs4955439	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4955443	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6446256	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6446257	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6769821	0.87[EUR][1000 genomes]
rs6778080	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6808036	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6809851	0.94[EUR][1000 genomes]
rs7429661	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7617480	0.81[AMR][1000 genomes]
rs7619016	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7626076	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7631586	0.85[EUR][1000 genomes]
rs9834003	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9867285	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv3349260	chr3:49284341-49284584	Weak transcription Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv3357795	chr3:49284503-49284850	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs12637346	AMT	cis	Nerve Tibial	GTEx
rs12637346	AMT	cis	Artery Tibial	GTEx
rs12637346	AMT	cis	lung	GTEx
rs12637346	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs12637346	AMT	cis	Esophagus Mucosa	GTEx
rs12637346	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs12637346	NICN1	cis	Thyroid	GTEx
rs12637346	NICN1-AS1	cis	Thyroid	GTEx
rs12637346	AMT	cis	Adipose Subcutaneous	GTEx
rs12637346	ARIH2	cis	Thyroid	GTEx
rs12637346	AMT	cis	Whole Blood	GTEx
rs12637346	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs12637346	AMT	cis	Thyroid	GTEx
rs12637346	AMT	cis	Muscle Skeletal	GTEx
rs12637346	PFKFB4	cis	Nerve Tibial	GTEx
rs12637346	AMT	cis	Artery Aorta	GTEx
rs12637346	AMT	cis	Esophagus Muscularis	GTEx
rs12637346	WDR6	cis	Nerve Tibial	GTEx
rs12637346	WDR6	cis	Muscle Skeletal	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49266200-49292600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:49276000-49285000	Weak transcription	Lung	lung
3	chr3:49276400-49286200	Weak transcription	NHDF-Ad	bronchial
4	chr3:49276400-49293400	Weak transcription	NHLF	lung
5	chr3:49276400-49306400	Weak transcription	Spleen	Spleen
6	chr3:49276600-49286200	Weak transcription	Right Ventricle	heart
7	chr3:49276600-49304000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:49277000-49286000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr3:49277400-49292600	Weak transcription	Fetal Intestine Large	intestine
10	chr3:49277800-49285600	Weak transcription	Placenta	Placenta
11	chr3:49278400-49285800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:49279600-49286200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:49280600-49286000	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:49281600-49285200	Strong transcription	Fetal Stomach	stomach
15	chr3:49282000-49285200	Strong transcription	Fetal Muscle Trunk	muscle
16	chr3:49282600-49286000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:49282600-49286000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:49282600-49286000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:49282600-49286000	Weak transcription	K562	blood
20	chr3:49282600-49286200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:49282600-49286200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:49282600-49286200	Weak transcription	GM12878-XiMat	blood
23	chr3:49282600-49286400	Weak transcription	Esophagus	oesophagus
24	chr3:49282600-49294800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:49282600-49299000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:49282600-49303200	Weak transcription	Left Ventricle	heart
27	chr3:49283000-49284600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr3:49283000-49286000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:49283000-49286000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:49283200-49286000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:49283200-49286000	Weak transcription	NHEK	skin
32	chr3:49283200-49286200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:49283400-49286200	Weak transcription	Ovary	ovary
34	chr3:49283400-49286200	Weak transcription	Hela-S3	cervix
35	chr3:49283400-49287400	Weak transcription	Osteobl	bone
36	chr3:49283400-49293200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:49283800-49285200	Weak transcription	Adipose Nuclei	Adipose
38	chr3:49284000-49285800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:49284200-49287400	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr3:49284400-49285200	Strong transcription	Fetal Muscle Leg	muscle

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