Variant report

Variant	rs9473557
Chromosome Location	chr6:49409737-49409738
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:49408141..49410231-chr6:49417787..49420122,2	K562	blood:
2	chr6:49409425..49411264-chr6:49414744..49417362,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10456622	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1141321	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196937	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12202075	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12209900	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12212022	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2086421	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2147570	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2448701	0.85[EUR][1000 genomes]
rs2448702	0.85[EUR][1000 genomes]
rs2448707	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2477405	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2477406	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2493440	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501961	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501962	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2501963	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2501977	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501979	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2501980	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3729619	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3806988	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3823114	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4267943	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4348317	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4458686	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4469291	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4573082	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715129	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715130	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715131	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60982898	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62411929	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411930	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411932	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458690	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458693	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458694	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6901278	0.85[EUR][1000 genomes]
rs6909128	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6923124	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744595	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750918	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7769018	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296616	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296617	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463473	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463474	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463475	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463476	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463477	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463479	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463480	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473547	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9473549	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9473551	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473552	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473553	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473560	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473561	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9473563	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473566	0.85[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	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv915806	chr6:49313295-49430422	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9473557	CENPQ	cis	Nerve Tibial	GTEx
rs9473557	MUT	cis	Artery Tibial	GTEx
rs9473557	CENPQ	cis	Thyroid	GTEx
rs9473557	MUT	Cis_1M	lymphoblastoid	RTeQTL
rs9473557	CENPQ	cis	Adipose Subcutaneous	GTEx
rs9473557	MUT	cis	Nerve Tibial	GTEx
rs9473557	CENPQ	cis	lung	GTEx
rs9473557	CENPQ	cis	Artery Tibial	GTEx
rs9473557	CENPQ	cis	Esophagus Muscularis	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49395400-49429800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:49396000-49420800	Strong transcription	Liver	Liver
3	chr6:49396000-49427400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:49396200-49420400	Strong transcription	Adipose Nuclei	Adipose
5	chr6:49396400-49429400	Weak transcription	Stomach Mucosa	stomach
6	chr6:49396600-49411000	Weak transcription	Fetal Heart	heart
7	chr6:49396600-49412400	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr6:49397000-49413800	Strong transcription	Duodenum Mucosa	Duodenum
9	chr6:49397000-49419800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr6:49397000-49425800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr6:49397000-49426600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:49397200-49421200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr6:49397400-49412600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:49397400-49425600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:49397400-49426000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr6:49397800-49419800	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr6:49397800-49420000	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:49398000-49412600	Strong transcription	Fetal Intestine Large	intestine
19	chr6:49398200-49429600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:49398400-49425600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:49398400-49427200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:49398600-49420000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:49398800-49412600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr6:49398800-49413200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:49398800-49418800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr6:49399000-49412600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:49399200-49412600	Strong transcription	Fetal Thymus	thymus
28	chr6:49399800-49412400	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr6:49399800-49420800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:49400400-49413600	Strong transcription	Stomach Smooth Muscle	stomach
31	chr6:49401000-49412600	Strong transcription	Placenta	Placenta
32	chr6:49401000-49422600	Weak transcription	GM12878-XiMat	blood
33	chr6:49401800-49413200	Strong transcription	Fetal Lung	lung
34	chr6:49402000-49412600	Strong transcription	Fetal Muscle Leg	muscle
35	chr6:49403000-49428800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:49403400-49411000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr6:49403400-49429600	Weak transcription	NHEK	skin
38	chr6:49404200-49429600	Weak transcription	Right Ventricle	heart
39	chr6:49405000-49423200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:49405800-49414400	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr6:49406200-49410000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:49406200-49413200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr6:49406400-49409800	Strong transcription	Ovary	ovary
44	chr6:49406400-49410000	Strong transcription	Brain Anterior Caudate	brain
45	chr6:49406400-49410000	Strong transcription	Left Ventricle	heart
46	chr6:49406400-49412400	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:49406600-49412600	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr6:49406600-49413800	Strong transcription	Dnd41	blood
49	chr6:49406800-49430400	Weak transcription	Esophagus	oesophagus
50	chr6:49407000-49412600	Strong transcription	HUES48 Cell Line	embryonic stem cell

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