Variant report

Variant	rs12665858
Chromosome Location	chr6:110446006-110446007
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11153226	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11751590	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11757055	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12110744	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12660119	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12660791	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12662013	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12665849	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1462490	0.83[ASN][1000 genomes]
rs1462492	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1462493	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2002630	0.92[ASN][1000 genomes]
rs4257894	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4299857	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4339500	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4509164	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4945850	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4945851	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4947048	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4947051	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4947058	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56122480	0.97[ASN][1000 genomes]
rs56135788	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56287427	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57983455	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60495849	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61020234	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6568633	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6913554	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6915379	0.95[ASN][1000 genomes]
rs6918148	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6925392	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6926540	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6927667	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6927697	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6927722	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6928684	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6938106	0.88[ASN][1000 genomes]
rs6938139	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6938653	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs719849	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73533834	0.83[ASN][1000 genomes]
rs73535810	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73535817	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73535821	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73535837	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73535838	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73537927	0.91[ASN][1000 genomes]
rs73537938	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73537949	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7744828	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7747842	0.80[ASN][1000 genomes]
rs7766850	0.81[ASN][1000 genomes]
rs9372248	0.81[ASN][1000 genomes]
rs9374156	0.83[ASN][1000 genomes]
rs9400359	0.83[ASN][1000 genomes]
rs9400360	0.83[ASN][1000 genomes]
rs9481047	0.81[ASN][1000 genomes]
rs9487317	0.81[ASN][1000 genomes]
rs9487318	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886535	chr6:110377006-110551463	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	esv2757188	chr6:110389926-110504680	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	esv2759462	chr6:110389926-110504680	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv1792799	chr6:110411065-110566597	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv886536	chr6:110426046-110502831	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv948824	chr6:110443685-110889332	Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12665858	WASF1	cis	Artery Tibial	GTEx
rs12665858	WASF1	cis	Muscle Skeletal	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110419000-110449600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr6:110419000-110461800	Weak transcription	HSMMtube	muscle
3	chr6:110419200-110449600	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:110423200-110448400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr6:110423400-110450000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:110423400-110459000	Weak transcription	Fetal Stomach	stomach
7	chr6:110423400-110459200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:110423400-110459200	Weak transcription	Aorta	Aorta
9	chr6:110425000-110456400	Weak transcription	HUVEC	blood vessel
10	chr6:110426800-110448000	Weak transcription	Pancreas	Pancrea
11	chr6:110427600-110459600	Weak transcription	NHEK	skin
12	chr6:110428200-110450000	Weak transcription	HepG2	liver
13	chr6:110429800-110453600	Weak transcription	Liver	Liver
14	chr6:110429800-110459200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:110430000-110446400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:110430000-110449800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:110430000-110452200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:110430400-110450200	Weak transcription	NHDF-Ad	bronchial
19	chr6:110431400-110459200	Weak transcription	HSMM	muscle
20	chr6:110436600-110449600	Weak transcription	Brain Anterior Caudate	brain
21	chr6:110436800-110449600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr6:110438000-110449800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:110438000-110449800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:110438000-110459200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:110441600-110463400	Weak transcription	A549	lung
26	chr6:110443000-110447000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:110443200-110446600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:110443200-110447200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:110443200-110449800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:110443400-110449800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:110443400-110452200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:110443600-110446600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:110443800-110449800	Weak transcription	Fetal Brain Male	brain
34	chr6:110443800-110459200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:110444000-110449600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:110444000-110449800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:110444000-110483800	Weak transcription	Fetal Kidney	kidney
38	chr6:110444200-110450000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:110444200-110459200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:110444200-110459200	Weak transcription	Ovary	ovary
41	chr6:110444600-110462000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:110444800-110446800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:110445000-110446200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
44	chr6:110445000-110446400	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:110445200-110446200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:110445200-110446400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:110445200-110450000	Weak transcription	Fetal Brain Female	brain
48	chr6:110445200-110459000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr6:110445200-110482400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:110445400-110446400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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