Variant report

Variant	rs9654010
Chromosome Location	chr3:49480908-49480909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1009051	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10155014	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10865956	0.84[EUR][1000 genomes]
rs1106620	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11130190	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11710434	0.83[AMR][1000 genomes]
rs11715060	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11719762	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11720542	0.83[AMR][1000 genomes]
rs11720657	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11923032	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11928090	0.84[EUR][1000 genomes]
rs12583	0.85[EUR][1000 genomes]
rs13096474	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13322887	0.88[EUR][1000 genomes]
rs1464569	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1982861	0.83[EUR][1000 genomes]
rs2140270	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2177268	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2312462	0.84[EUR][1000 genomes]
rs2329025	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3448	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3866330	0.84[EUR][1000 genomes]
rs3870339	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3870341	0.84[EUR][1000 genomes]
rs3905330	0.87[EUR][1000 genomes]
rs4052546	0.85[EUR][1000 genomes]
rs4241407	0.84[EUR][1000 genomes]
rs4855837	0.82[EUR][1000 genomes]
rs4855853	0.84[EUR][1000 genomes]
rs4855858	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4855869	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4955413	0.80[AFR][1000 genomes]
rs4955430	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56127630	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57273516	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62259933	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62259943	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62259944	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62259947	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62261183	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62261249	0.84[EUR][1000 genomes]
rs6446262	0.81[EUR][1000 genomes]
rs6446275	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6769744	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6783003	0.89[EUR][1000 genomes]
rs6785045	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6796147	0.81[EUR][1000 genomes]
rs6805609	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72934271	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73073004	0.80[EUR][1000 genomes]
rs73088137	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7355800	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7374731	0.87[EUR][1000 genomes]
rs7613491	0.91[EUR][1000 genomes]
rs7619789	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7620024	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7622786	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7625857	0.82[EUR][1000 genomes]
rs7638750	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7644148	0.86[EUR][1000 genomes]
rs7647973	0.91[EUR][1000 genomes]
rs7648995	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7651372	0.88[EUR][1000 genomes]
rs8897	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs940045	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs974495	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9809237	0.87[EUR][1000 genomes]
rs9817807	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9842132	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9860055	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9861027	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9862534	0.84[EUR][1000 genomes]
rs9871024	0.88[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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv963482	chr3:49459177-49486938	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs9654010	WDR6	cis	Nerve Tibial	GTEx
rs9654010	AMT	cis	Esophagus Muscularis	GTEx
rs9654010	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs9654010	AMT	cis	lung	GTEx
rs9654010	AMT	cis	Adipose Subcutaneous	GTEx
rs9654010	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs9654010	AMT	cis	Whole Blood	GTEx
rs9654010	AMT	cis	Artery Aorta	GTEx
rs9654010	AMT	cis	Nerve Tibial	GTEx
rs9654010	AMT	cis	Thyroid	GTEx
rs9654010	NICN1-AS1	cis	Thyroid	GTEx
rs9654010	AMT	cis	Artery Tibial	GTEx
rs9654010	WDR6	cis	Muscle Skeletal	GTEx
rs9654010	AMT	cis	Esophagus Mucosa	GTEx
rs9654010	NICN1	cis	Thyroid	GTEx
rs9654010	AMT	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49467400-49486400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:49467800-49481000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:49467800-49481200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:49480000-49484200	Enhancers	Placenta	Placenta
5	chr3:49480400-49481600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:49480400-49481600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:49480400-49484400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:49480400-49484400	Enhancers	Primary B cells from cord blood	blood
9	chr3:49480800-49481000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:49480800-49481200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:49480800-49481400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:49480800-49481600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr3:49480800-49481600	Enhancers	NHDF-Ad	bronchial
14	chr3:49480800-49482000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:49480800-49482200	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr3:49480800-49482400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr3:49480800-49482400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:49480800-49482400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:49480800-49482600	Enhancers	Primary T cells fromperipheralblood	blood
20	chr3:49480800-49482600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:49480800-49482600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr3:49480800-49482600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:49480800-49482600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:49480800-49482600	Enhancers	GM12878-XiMat	blood
25	chr3:49480800-49482800	Enhancers	Primary B cells from peripheral blood	blood

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