Variant report

Variant	rs62411930
Chromosome Location	chr6:49420248-49420249
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	chr6:49412522..49414026-chr6:49419291..49421215,2	MCF-7	breast:
2	chr6:49419838..49421598-chr6:49428414..49430900,2	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	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1141321	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196937	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12202075	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12209900	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12212022	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2086421	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2147570	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2448701	0.83[EUR][1000 genomes]
rs2448702	0.83[EUR][1000 genomes]
rs2448707	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2477405	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2477406	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2493440	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501961	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501962	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2501963	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2501977	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501979	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2501980	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3729619	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3806988	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3823114	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4267943	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4348317	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4458686	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4469291	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4573082	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715129	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715130	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715131	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60982898	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62411929	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411932	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458690	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458693	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458694	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6901278	0.82[EUR][1000 genomes]
rs6909128	0.92[ASN][1000 genomes]
rs6923124	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744595	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750918	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7769018	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296616	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296617	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463473	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463474	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463475	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463476	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463477	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463479	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463480	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463483	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473547	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9473549	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9473551	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473552	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473553	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473555	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473557	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473560	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473561	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9473563	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473566	0.82[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
rs62411930	MUT	cis	Artery Tibial	GTEx
rs62411930	CENPQ	cis	Adipose Subcutaneous	GTEx
rs62411930	CENPQ	cis	Esophagus Muscularis	GTEx
rs62411930	MUT	cis	Nerve Tibial	GTEx
rs62411930	CENPQ	cis	Artery Tibial	GTEx
rs62411930	CENPQ	cis	Nerve Tibial	GTEx
rs62411930	CENPQ	cis	lung	GTEx
rs62411930	CENPQ	cis	Thyroid	GTEx
rs62411930	MUT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 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	chr6:49397000-49425800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr6:49397000-49426600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:49397200-49421200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr6:49397400-49425600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:49397400-49426000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:49398200-49429600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:49398400-49425600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:49398400-49427200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:49399800-49420800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:49401000-49422600	Weak transcription	GM12878-XiMat	blood
16	chr6:49403000-49428800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:49403400-49429600	Weak transcription	NHEK	skin
18	chr6:49404200-49429600	Weak transcription	Right Ventricle	heart
19	chr6:49405000-49423200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:49406800-49430400	Weak transcription	Esophagus	oesophagus
21	chr6:49407600-49428800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:49407800-49430400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:49407800-49430400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:49407800-49430400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:49407800-49430400	Weak transcription	Lung	lung
26	chr6:49408000-49428200	Weak transcription	Fetal Brain Male	brain
27	chr6:49408000-49429200	Weak transcription	Thymus	Thymus
28	chr6:49408000-49430400	Weak transcription	Gastric	stomach
29	chr6:49408200-49428000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr6:49408200-49429400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:49408200-49429600	Weak transcription	Hela-S3	cervix
32	chr6:49408400-49422400	Weak transcription	Spleen	Spleen
33	chr6:49408600-49422000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:49408600-49429600	Weak transcription	K562	blood
35	chr6:49408800-49429200	Weak transcription	Small Intestine	intestine
36	chr6:49408800-49429400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr6:49408800-49429600	Weak transcription	HSMMtube	muscle
38	chr6:49408800-49430000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:49409000-49421800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr6:49409000-49426200	Weak transcription	NHLF	lung
41	chr6:49409000-49429600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr6:49409200-49424600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:49409200-49430400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:49409600-49429600	Weak transcription	Colonic Mucosa	Colon
45	chr6:49410400-49430400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:49411200-49422000	Weak transcription	Left Ventricle	heart
47	chr6:49411200-49428800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr6:49412000-49429200	Weak transcription	Psoas Muscle	Psoas
49	chr6:49412000-49429600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:49412400-49421800	Weak transcription	Colon Smooth Muscle	Colon

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