Variant report

Variant	rs9296617
Chromosome Location	chr6:49428360-49428361
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:49428313-49428363	NH-A	brain:	n/a
2	chr6:49428313-49428363	HL-60	blood:	n/a
3	chr6:49428313-49428363	T-47D	breast:	n/a
4	chr6:49428313-49428363	SK-N-SH_RA	brain:	n/a
5	chr6:49428313-49428363	SKMC	muscle:	n/a
6	chr6:49428313-49428363	AG04450	lung:	fetal
7	chr6:49428313-49428363	GM06990	blood:	n/a
8	chr6:49428313-49428363	CMK	blood:	n/a
9	chr6:49428313-49428363	H1-hESC	embryonic stem cell:	embryo
10	chr6:49428313-49428363	AG09319	gingival:	n/a
11	chr6:49428313-49428363	SK-N-SH	brain:	n/a
12	chr6:49428313-49428363	K562	blood:	n/a
13	chr6:49428313-49428363	HUVEC	blood vessel:	n/a
14	chr6:49428313-49428363	HRCEpiC	kidney:	n/a
15	chr6:49428313-49428363	BE2_C	brain:	n/a
16	chr6:49428313-49428363	IMR90	lung:	fetal
17	chr6:49428313-49428363	GM12891	blood:	n/a
18	chr6:49428313-49428363	AG10803	skin:	n/a
19	chr6:49428313-49428363	BJ	skin:	n/a
20	chr6:49428313-49428363	GM12892	blood:	n/a
21	chr6:49428313-49428363	AG09309	skin:	n/a
22	chr6:49428313-49428363	HRE	kidney:	n/a
23	chr6:49428313-49428363	MCF-7	breast:	n/a
24	chr6:49428313-49428363	NT2-D1	testis:	n/a
25	chr6:49428313-49428363	HCM	heart:	n/a
26	chr6:49428313-49428363	HEK293	kidney:	embryo
27	chr6:49428313-49428363	Jurkat	blood:	n/a
28	chr6:49428313-49428363	PrEC	prostate:	n/a
29	chr6:49428313-49428363	Hepatocyte	liver:	n/a
30	chr6:49428313-49428363	Caco-2	colon:	n/a
31	chr6:49428313-49428363	HCF	heart:	n/a
32	chr6:49428313-49428363	ovcar-3	ovarian:	n/a
33	chr6:49428313-49428363	AG04449	skin:	fetal
34	chr6:49428313-49428363	HNPCEpiC	eye:	n/a
35	chr6:49428313-49428363	PANC-1	pancreas:	n/a
36	chr6:49428313-49428363	PFSK-1	brain:	n/a
37	chr6:49428313-49428363	LNCaP	prostate:	n/a
38	chr6:49428313-49428363	SAEC	small airway:	n/a
39	chr6:49428313-49428363	MCF10A-Er-Src	breast:	n/a
40	chr6:49428313-49428363	Hela-S3	cervix:	n/a
41	chr6:49428313-49428363	HIPEpiC	eye:	n/a
42	chr6:49428313-49428363	U87	brain:	n/a
43	chr6:49428313-49428363	HPAEpiC	pulmonary alveolar:	n/a
44	chr6:49428313-49428363	HMEC	breast:	n/a
45	chr6:49428313-49428363	HepG2	liver:	n/a
46	chr6:49428313-49428363	HRPEpiC	eye:	n/a
47	chr6:49428313-49428363	NB4	blood:	n/a
48	chr6:49428313-49428363	A549	lung:	n/a
49	chr6:49428313-49428363	HEEpiC	esophagus:	n/a
50	chr6:49428313-49428363	RPTEC	kidney:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:49352086..49353625-chr6:49427377..49430292,2	K562	blood:
2	chr6:49428075..49430840-chr6:49629508..49632761,3	K562	blood:
3	chr6:49427543..49430477-chr6:49436132..49438156,2	K562	blood:

No data

Variant related genes	Relation type
CENPQ	CpG island

Extended variants
information (count: 72 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10456622	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1141321	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12196937	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12202075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209900	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212022	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2086421	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2147570	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2448701	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2448702	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2448707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477405	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2477406	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2493440	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2501961	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2501962	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501963	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2501977	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2501979	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2501980	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3729619	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3806988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3823114	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3957334	0.81[EUR][1000 genomes]
rs3997172	0.81[EUR][1000 genomes]
rs4267943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4348317	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4458686	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4469291	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4573082	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4715129	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4715130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4715131	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60944851	0.81[EUR][1000 genomes]
rs60982898	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62411929	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62411930	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62411932	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458690	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458693	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458694	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901278	0.87[EUR][1000 genomes]
rs6909128	0.88[ASN][1000 genomes]
rs6923124	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7744595	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7750918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769018	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296616	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463473	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9463474	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9463475	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9463476	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9463477	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9463479	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463480	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463483	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473547	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9473549	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9473551	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9473552	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9473553	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473555	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473557	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9473563	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473566	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	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
5	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9296617	CENPQ	cis	Adipose Subcutaneous	GTEx
rs9296617	MUT	cis	Nerve Tibial	GTEx
rs9296617	CENPQ	cis	Esophagus Muscularis	GTEx
rs9296617	MUT	cis	Artery Tibial	GTEx
rs9296617	MUT	Cis_1M	lymphoblastoid	RTeQTL
rs9296617	CENPQ	cis	Thyroid	GTEx
rs9296617	CENPQ	cis	Nerve Tibial	GTEx
rs9296617	CENPQ	cis	lung	GTEx
rs9296617	CENPQ	cis	Artery Tibial	GTEx
rs9296617	MUT	cis	multi-tissue	Pritchard

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	chr6:49396400-49429400	Weak transcription	Stomach Mucosa	stomach
3	chr6:49398200-49429600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:49403000-49428800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:49403400-49429600	Weak transcription	NHEK	skin
6	chr6:49404200-49429600	Weak transcription	Right Ventricle	heart
7	chr6:49406800-49430400	Weak transcription	Esophagus	oesophagus
8	chr6:49407600-49428800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:49407800-49430400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:49407800-49430400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:49407800-49430400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:49407800-49430400	Weak transcription	Lung	lung
13	chr6:49408000-49429200	Weak transcription	Thymus	Thymus
14	chr6:49408000-49430400	Weak transcription	Gastric	stomach
15	chr6:49408200-49429400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:49408200-49429600	Weak transcription	Hela-S3	cervix
17	chr6:49408600-49429600	Weak transcription	K562	blood
18	chr6:49408800-49429200	Weak transcription	Small Intestine	intestine
19	chr6:49408800-49429400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:49408800-49429600	Weak transcription	HSMMtube	muscle
21	chr6:49408800-49430000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:49409000-49429600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:49409200-49430400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:49409600-49429600	Weak transcription	Colonic Mucosa	Colon
25	chr6:49410400-49430400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:49411200-49428800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:49412000-49429200	Weak transcription	Psoas Muscle	Psoas
28	chr6:49412000-49429600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:49412600-49429200	Weak transcription	Pancreas	Pancrea
30	chr6:49412600-49429400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr6:49412600-49429600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr6:49412600-49429600	Weak transcription	Fetal Heart	heart
33	chr6:49416400-49429600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:49416400-49429600	Weak transcription	HMEC	breast
35	chr6:49416600-49429600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr6:49416800-49429600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr6:49418800-49428800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr6:49418800-49429600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:49419800-49430000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:49420800-49429600	Weak transcription	Osteobl	bone
41	chr6:49421600-49429600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:49422600-49429400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr6:49422800-49428800	Weak transcription	Fetal Stomach	stomach
44	chr6:49422800-49429200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr6:49422800-49429400	Weak transcription	Fetal Intestine Small	intestine
46	chr6:49423200-49429200	Weak transcription	Spleen	Spleen
47	chr6:49423200-49429800	Weak transcription	Aorta	Aorta
48	chr6:49423400-49429200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr6:49423400-49429400	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:49423400-49429800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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