Variant report

Variant	rs9349491
Chromosome Location	chr6:49436199-49436200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:49434330..49436569-chr6:49445501..49447295,2	K562	blood:
2	chr6:49430814..49434554-chr6:49435303..49440470,7	K562	blood:
3	chr6:49431034..49433183-chr6:49434842..49436900,4	MCF-7	breast:
4	chr6:49428636..49430625-chr6:49435581..49438306,2	MCF-7	breast:
5	chr6:49427543..49430477-chr6:49436132..49438156,2	K562	blood:
6	chr6:49423687..49425386-chr6:49433841..49436360,2	K562	blood:
7	chr6:49435298..49437139-chr6:49437563..49440093,3	K562	blood:

Variant related genes	Relation type
ENSG00000146085	Chromatin interaction
ENSG00000031691	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs12528625	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1471539	0.88[EUR][1000 genomes]
rs2229384	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2251115	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2448704	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2448705	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2493441	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2501959	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2501960	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501964	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2501965	0.88[EUR][1000 genomes]
rs2501966	0.88[EUR][1000 genomes]
rs2501968	0.88[EUR][1000 genomes]
rs2501978	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6458685	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6458688	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6902429	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6915187	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6916888	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6918347	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6921413	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7759071	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7767725	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7774688	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8589	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9369898	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9381784	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9381787	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9381788	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9381789	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9395492	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9395493	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463478	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9463482	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9473550	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv603081	chr6:49421241-49446233	Weak transcription Active TSS Enhancers Flanking 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	10 gene(s)	inside rSNPs	diseases
4	nsv603082	chr6:49421241-49446509	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv603083	chr6:49429706-49446233	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv603084	chr6:49429706-49446509	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv603085	chr6:49429706-49450341	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv441996	chr6:49431565-49447295	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	nsv603086	chr6:49431569-49440363	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv603087	chr6:49431569-49441062	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	nsv603088	chr6:49431569-49446504	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv603089	chr6:49431569-49446509	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	esv2763934	chr6:49431569-49447295	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
14	nsv603090	chr6:49431569-49447295	Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
15	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9349491	CENPQ	cis	lung	GTEx
rs9349491	MUT	cis	Artery Tibial	GTEx
rs9349491	CENPQ	Cis_1M	lymphoblastoid	RTeQTL
rs9349491	CENPQ	cis	Nerve Tibial	GTEx
rs9349491	CENPQ	cis	Artery Tibial	GTEx
rs9349491	CENPQ	cis	Esophagus Mucosa	GTEx
rs9349491	CENPQ	cis	Artery Aorta	GTEx
rs9349491	CENPQ	cis	Whole Blood	GTEx
rs9349491	CENPQ	cis	Muscle Skeletal	GTEx
rs9349491	MUT	cis	Nerve Tibial	GTEx
rs9349491	CENPQ	cis	Esophagus Muscularis	GTEx
rs9349491	CENPQ	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49431600-49449200	Weak transcription	Spleen	Spleen
2	chr6:49431800-49449000	Weak transcription	Esophagus	oesophagus
3	chr6:49431800-49456400	Weak transcription	Placenta	Placenta
4	chr6:49431800-49456600	Weak transcription	Left Ventricle	heart
5	chr6:49431800-49461200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:49431800-49462000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:49432000-49438800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:49432000-49439000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:49432000-49439200	Weak transcription	Fetal Thymus	thymus
10	chr6:49432000-49451400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:49432000-49456200	Weak transcription	Brain Anterior Caudate	brain
12	chr6:49432000-49456400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:49432000-49457600	Weak transcription	HSMM	muscle
14	chr6:49432000-49459600	Weak transcription	Small Intestine	intestine
15	chr6:49432000-49462000	Weak transcription	Brain Angular Gyrus	brain
16	chr6:49432000-49463000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr6:49432200-49438400	Weak transcription	Liver	Liver
18	chr6:49432200-49438600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:49432200-49438800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr6:49432200-49439000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:49432200-49439200	Weak transcription	Adipose Nuclei	Adipose
22	chr6:49432200-49439800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr6:49432200-49439800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:49432200-49440000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:49432200-49442800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr6:49432200-49449200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:49432200-49449200	Weak transcription	Fetal Intestine Small	intestine
28	chr6:49432200-49449400	Weak transcription	Ovary	ovary
29	chr6:49432200-49449600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:49432200-49452400	Weak transcription	Primary T cells from cord blood	blood
31	chr6:49432200-49456200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:49432200-49456400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:49432200-49456400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr6:49432200-49456600	Weak transcription	NH-A	brain
35	chr6:49432200-49457400	Weak transcription	Brain Germinal Matrix	brain
36	chr6:49432200-49461600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:49432200-49462400	Weak transcription	Fetal Lung	lung
38	chr6:49432200-49462800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr6:49432200-49463800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:49432200-49465000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:49432400-49438600	Weak transcription	HUVEC	blood vessel
42	chr6:49432400-49438800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:49432400-49438800	Weak transcription	A549	lung
44	chr6:49432400-49438800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr6:49432400-49439000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:49432400-49439200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr6:49432400-49439800	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr6:49432400-49439800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr6:49432400-49448800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:49432400-49456400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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