Variant report

Variant	rs2229384
Chromosome Location	chr6:49425521-49425522
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:49423228..49426093-chr6:49579151..49581831,2	K562	blood:
2	chr6:49425386..49427485-chr6:49429135..49431175,2	MCF-7	breast:
3	chr6:49424647..49427636-chr6:49428636..49431243,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146085	Chromatin interaction
ENSG00000031691	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 17 )

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

rs_ID	r²[population]
rs12528625	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1471539	0.82[ASW][hapmap];0.87[CEU][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2251115	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448705	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2493441	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2501959	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501960	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2501964	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501965	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2501966	0.81[ASW][hapmap];0.88[CEU][hapmap];0.84[GIH][hapmap];0.98[LWK][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2501968	0.82[ASW][hapmap];0.88[CEU][hapmap];0.84[GIH][hapmap];0.98[LWK][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2501978	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458685	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458688	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6902429	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6915187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916888	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6918347	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6921413	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7759071	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767725	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774688	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8589	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9349491	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9369898	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9381784	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9381787	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9381788	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9381789	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9395492	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463478	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9463482	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9473550	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2229384	CENPQ	cis	Nerve Tibial	GTEx
rs2229384	MUT	cis	cerebellum	SCAN
rs2229384	CENPQ	cis	lymphoblastoid	seeQTL
rs2229384	CENPQ	cis	Whole Blood	GTEx
rs2229384	CENPQ	cis	Artery Tibial	GTEx
rs2229384	CENPQ	cis	lung	GTEx
rs2229384	CENPQ	cis	Esophagus Muscularis	GTEx
rs2229384	MUT	cis	multi-tissue	Pritchard
rs2229384	CENPQ	cis	Muscle Skeletal	GTEx
rs2229384	CENPQ	cis	Artery Aorta	GTEx
rs2229384	C6orf139	cis	normal skin	skin_eQTL
rs2229384	C6orf139	cis	multi-tissue	Pritchard
rs2229384	MUT	cis	Artery Tibial	GTEx
rs2229384	MUT	cis	Nerve Tibial	GTEx
rs2229384	CENPQ	cis	Adipose Subcutaneous	GTEx
rs2229384	CENPQ	cis	Esophagus Mucosa	GTEx
rs2229384	CENPQ	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	chr6:49396000-49427400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:49396400-49429400	Weak transcription	Stomach Mucosa	stomach
4	chr6:49397000-49425800	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr6:49397000-49426600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:49397400-49425600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:49397400-49426000	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:49398200-49429600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:49398400-49425600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:49398400-49427200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:49403000-49428800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:49403400-49429600	Weak transcription	NHEK	skin
13	chr6:49404200-49429600	Weak transcription	Right Ventricle	heart
14	chr6:49406800-49430400	Weak transcription	Esophagus	oesophagus
15	chr6:49407600-49428800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr6:49407800-49430400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:49407800-49430400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:49407800-49430400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:49407800-49430400	Weak transcription	Lung	lung
20	chr6:49408000-49428200	Weak transcription	Fetal Brain Male	brain
21	chr6:49408000-49429200	Weak transcription	Thymus	Thymus
22	chr6:49408000-49430400	Weak transcription	Gastric	stomach
23	chr6:49408200-49428000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr6:49408200-49429400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:49408200-49429600	Weak transcription	Hela-S3	cervix
26	chr6:49408600-49429600	Weak transcription	K562	blood
27	chr6:49408800-49429200	Weak transcription	Small Intestine	intestine
28	chr6:49408800-49429400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:49408800-49429600	Weak transcription	HSMMtube	muscle
30	chr6:49408800-49430000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:49409000-49426200	Weak transcription	NHLF	lung
32	chr6:49409000-49429600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr6:49409200-49430400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:49409600-49429600	Weak transcription	Colonic Mucosa	Colon
35	chr6:49410400-49430400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr6:49411200-49428800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr6:49412000-49429200	Weak transcription	Psoas Muscle	Psoas
38	chr6:49412000-49429600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:49412600-49426400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:49412600-49429200	Weak transcription	Pancreas	Pancrea
41	chr6:49412600-49429400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr6:49412600-49429600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr6:49412600-49429600	Weak transcription	Fetal Heart	heart
44	chr6:49414400-49428200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:49416200-49427000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:49416400-49427600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr6:49416400-49429600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:49416400-49429600	Weak transcription	HMEC	breast
49	chr6:49416600-49429600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr6:49416800-49429600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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