Variant report

Variant	rs2501964
Chromosome Location	chr6:49454667-49454668
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:49428409..49430841-chr6:49452599..49454961,2	K562	blood:
2	chr6:49431070..49433020-chr6:49452542..49455281,2	K562	blood:

Variant related genes	Relation type
ENSG00000031691	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12528625	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1471539	0.84[EUR][1000 genomes]
rs2229384	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2251115	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2448704	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2448705	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2493441	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2501959	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501960	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2501965	0.84[EUR][1000 genomes]
rs2501966	0.84[EUR][1000 genomes]
rs2501968	0.84[EUR][1000 genomes]
rs2501978	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6458685	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6458688	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6902429	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6915187	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6916888	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6918347	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6921413	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7759071	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7767725	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7774688	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8589	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9349491	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9369898	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9381784	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9381787	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9381788	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9381789	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9395492	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9395493	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463478	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9463482	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9473550	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1019611	chr6:49431569-49470663	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	nsv885881	chr6:49439805-49575141	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2501964	CENPQ	cis	Esophagus Muscularis	GTEx
rs2501964	CENPQ	cis	Artery Aorta	GTEx
rs2501964	MUT	cis	Artery Tibial	GTEx
rs2501964	CENPQ	cis	lung	GTEx
rs2501964	MUT	cis	Nerve Tibial	GTEx
rs2501964	CENPQ	cis	Adipose Subcutaneous	GTEx
rs2501964	CENPQ	cis	Nerve Tibial	GTEx
rs2501964	CENPQ	cis	Muscle Skeletal	GTEx
rs2501964	CENPQ	Cis_1M	lymphoblastoid	RTeQTL
rs2501964	CENPQ	cis	Esophagus Mucosa	GTEx
rs2501964	CENPQ	cis	Artery Tibial	GTEx
rs2501964	CENPQ	cis	Whole Blood	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49431800-49456400	Weak transcription	Placenta	Placenta
2	chr6:49431800-49456600	Weak transcription	Left Ventricle	heart
3	chr6:49431800-49461200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:49431800-49462000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:49432000-49456200	Weak transcription	Brain Anterior Caudate	brain
6	chr6:49432000-49456400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:49432000-49457600	Weak transcription	HSMM	muscle
8	chr6:49432000-49459600	Weak transcription	Small Intestine	intestine
9	chr6:49432000-49462000	Weak transcription	Brain Angular Gyrus	brain
10	chr6:49432000-49463000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:49432200-49456200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:49432200-49456400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:49432200-49456400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:49432200-49456600	Weak transcription	NH-A	brain
15	chr6:49432200-49457400	Weak transcription	Brain Germinal Matrix	brain
16	chr6:49432200-49461600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:49432200-49462400	Weak transcription	Fetal Lung	lung
18	chr6:49432200-49462800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr6:49432200-49463800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:49432200-49465000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:49432400-49456400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:49432600-49456000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:49432600-49456000	Weak transcription	HMEC	breast
24	chr6:49432600-49456400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:49432600-49456400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr6:49432600-49456800	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:49432600-49460600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr6:49432600-49472000	Weak transcription	NHEK	skin
29	chr6:49433200-49459600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:49433200-49461200	Weak transcription	NHDF-Ad	bronchial
31	chr6:49433600-49458600	Weak transcription	Hela-S3	cervix
32	chr6:49434200-49456400	Weak transcription	GM12878-XiMat	blood
33	chr6:49437400-49456400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:49439400-49456600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr6:49440400-49460000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr6:49440400-49465200	Weak transcription	HUVEC	blood vessel
37	chr6:49440800-49455200	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr6:49441000-49456200	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr6:49441000-49456400	Weak transcription	Liver	Liver
40	chr6:49441000-49456400	Weak transcription	K562	blood
41	chr6:49441000-49464200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:49441200-49456200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr6:49441200-49456200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:49441200-49456400	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr6:49441200-49461800	Weak transcription	A549	lung
46	chr6:49441400-49456400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:49441400-49456400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr6:49442000-49456400	Weak transcription	Adipose Nuclei	Adipose
49	chr6:49442200-49455200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr6:49443200-49457600	Weak transcription	Fetal Brain Female	brain

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