Variant report

Variant	rs2501966
Chromosome Location	chr6:49457835-49457836
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	chr6:49429806..49431359-chr6:49457434..49460019,2	K562	blood:

Variant related genes	Relation type
ENSG00000031691	Chromatin interaction
ENSG00000146085	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10755760	0.88[ASN][1000 genomes]
rs12528625	0.80[EUR][1000 genomes]
rs1471539	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1480614	0.87[ASN][1000 genomes]
rs2127755	0.87[ASN][1000 genomes]
rs2229384	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]
rs2251115	0.88[ASW][hapmap];0.88[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2396911	0.87[ASN][1000 genomes]
rs2448704	0.87[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2448705	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2493441	0.83[EUR][1000 genomes]
rs2501959	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2501960	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2501964	0.84[EUR][1000 genomes]
rs2501965	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501978	0.85[EUR][1000 genomes]
rs4367370	0.87[ASN][1000 genomes]
rs6458685	0.87[EUR][1000 genomes]
rs6458688	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6902429	0.88[EUR][1000 genomes]
rs6915187	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6916888	0.88[EUR][1000 genomes]
rs6918347	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6921413	0.88[EUR][1000 genomes]
rs7453050	0.87[ASN][1000 genomes]
rs7759071	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7767725	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7774688	0.85[EUR][1000 genomes]
rs8589	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9349491	0.88[EUR][1000 genomes]
rs9369898	0.87[EUR][1000 genomes]
rs9381784	0.84[CEU][hapmap];0.82[CHB][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs9381787	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9381788	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9381789	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9395492	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9395493	0.88[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9463478	0.88[EUR][1000 genomes]
rs9463482	0.86[EUR][1000 genomes]
rs9463489	0.88[ASN][1000 genomes]
rs9463492	0.87[ASN][1000 genomes]
rs9463493	0.87[ASN][1000 genomes]
rs9473550	0.83[EUR][1000 genomes]
rs9473568	0.88[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2501966	CENPQ	cis	lymphoblastoid	seeQTL
rs2501966	CENPQ	cis	lung	GTEx
rs2501966	CENPQ	cis	Esophagus Muscularis	GTEx
rs2501966	CENPQ	cis	Artery Aorta	GTEx
rs2501966	MUT	cis	Nerve Tibial	GTEx
rs2501966	CENPQ	Cis_1M	lymphoblastoid	RTeQTL
rs2501966	CENPQ	cis	multi-tissue	Pritchard
rs2501966	C6orf139	cis	multi-tissue	Pritchard
rs2501966	CENPQ	cis	Muscle Skeletal	GTEx
rs2501966	CENPQ	cis	Whole Blood	GTEx
rs2501966	MUT	cis	cerebellum	SCAN
rs2501966	CENPQ	cis	Adipose Subcutaneous	GTEx
rs2501966	MUT	cis	multi-tissue	Pritchard
rs2501966	CENPQ	cis	Esophagus Mucosa	GTEx
rs2501966	CENPQ	cis	Nerve Tibial	GTEx
rs2501966	CENPQ	cis	Artery Tibial	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49431800-49461200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:49431800-49462000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:49432000-49459600	Weak transcription	Small Intestine	intestine
4	chr6:49432000-49462000	Weak transcription	Brain Angular Gyrus	brain
5	chr6:49432000-49463000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr6:49432200-49461600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:49432200-49462400	Weak transcription	Fetal Lung	lung
8	chr6:49432200-49462800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr6:49432200-49463800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:49432200-49465000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:49432600-49460600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:49432600-49472000	Weak transcription	NHEK	skin
13	chr6:49433200-49459600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:49433200-49461200	Weak transcription	NHDF-Ad	bronchial
15	chr6:49433600-49458600	Weak transcription	Hela-S3	cervix
16	chr6:49440400-49460000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:49440400-49465200	Weak transcription	HUVEC	blood vessel
18	chr6:49441000-49464200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:49441200-49461800	Weak transcription	A549	lung
20	chr6:49446000-49460200	Weak transcription	Stomach Mucosa	stomach
21	chr6:49446800-49461800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:49447400-49458200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:49447800-49458000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:49447800-49460400	Weak transcription	Right Ventricle	heart
25	chr6:49448000-49459800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:49448400-49464600	Weak transcription	Gastric	stomach
27	chr6:49448600-49460400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:49449400-49460200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:49449800-49463000	Weak transcription	Lung	lung
30	chr6:49449800-49465000	Weak transcription	Fetal Muscle Leg	muscle
31	chr6:49450400-49458600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:49450400-49461400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:49450400-49464200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:49450600-49462600	Weak transcription	Thymus	Thymus
35	chr6:49450600-49464000	Weak transcription	Spleen	Spleen
36	chr6:49451000-49461800	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:49451400-49467400	Weak transcription	Fetal Intestine Small	intestine
38	chr6:49451600-49464000	Weak transcription	Fetal Stomach	stomach
39	chr6:49453800-49462000	Strong transcription	Dnd41	blood
40	chr6:49454000-49465200	Weak transcription	Fetal Brain Male	brain
41	chr6:49454800-49463400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr6:49455000-49462200	Weak transcription	Psoas Muscle	Psoas
43	chr6:49455200-49459000	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr6:49455200-49460000	Weak transcription	Osteobl	bone
45	chr6:49455200-49460400	Strong transcription	Primary T cells from cord blood	blood
46	chr6:49455200-49461600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr6:49455200-49463600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:49455400-49461400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:49455600-49460600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:49455600-49461800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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