Variant report

Variant	rs6458454
Chromosome Location	chr6:45587779-45587780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45586124..45588757-chr6:45593642..45595317,2	K562	blood:
2	chr6:45575640..45578537-chr6:45586483..45588913,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10080253	0.82[ASN][1000 genomes]
rs12528502	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12661124	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12663210	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12665637	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1491142	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16873543	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16873550	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs16873554	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2020084	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56083876	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57939401	0.80[ASN][1000 genomes]
rs58939587	0.80[ASN][1000 genomes]
rs59074904	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60540355	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60884282	0.82[ASN][1000 genomes]
rs6458449	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6458450	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458453	0.85[ASN][1000 genomes]
rs6458455	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6899443	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6930188	0.83[ASN][1000 genomes]
rs6934210	0.82[ASN][1000 genomes]
rs6936365	0.85[ASN][1000 genomes]
rs6938247	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs6938489	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6941971	0.80[ASN][1000 genomes]
rs713270	0.85[ASN][1000 genomes]
rs73457129	0.86[AFR][1000 genomes]
rs73738526	0.85[ASN][1000 genomes]
rs73738527	0.80[ASN][1000 genomes]
rs7742335	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7752183	0.80[ASN][1000 genomes]
rs7752200	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7758915	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7759415	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7760394	0.84[AFR][1000 genomes]
rs7763886	0.82[ASN][1000 genomes]
rs7764338	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs7766534	0.80[ASN][1000 genomes]
rs7768962	0.80[ASN][1000 genomes]
rs9296462	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9296463	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9463108	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9472518	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9472521	0.80[ASN][1000 genomes]
rs9472524	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9472525	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9472527	0.80[ASN][1000 genomes]
rs9472530	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9472531	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9472532	0.82[ASN][1000 genomes]
rs9472534	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[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	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv427755	chr6:45474631-45627025	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6458454	SPATA20	trans	lymphoblastoid	seeQTL
rs6458454	ENPP4	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45579000-45587800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr6:45582800-45588200	Weak transcription	Fetal Lung	lung
3	chr6:45583200-45587800	Weak transcription	NHEK	skin
4	chr6:45584600-45588600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:45584600-45589000	Enhancers	HSMM	muscle
6	chr6:45586000-45588000	Weak transcription	Hela-S3	cervix
7	chr6:45586400-45587800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:45587000-45588400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:45587000-45588400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:45587000-45588600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr6:45587200-45588600	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr6:45587200-45588600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr6:45587200-45588600	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr6:45587200-45588600	Enhancers	NHLF	lung
15	chr6:45587200-45588600	Enhancers	Osteobl	bone
16	chr6:45587200-45589000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:45587200-45589000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr6:45587200-45589200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr6:45587400-45588400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:45587400-45588400	Enhancers	Duodenum Mucosa	Duodenum
21	chr6:45587400-45588400	Enhancers	NH-A	brain
22	chr6:45587400-45588600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:45587400-45588600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:45587400-45588600	Enhancers	NHDF-Ad	bronchial
25	chr6:45587400-45588800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr6:45587400-45588800	Enhancers	HSMMtube	muscle
27	chr6:45587400-45589000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr6:45587400-45589000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr6:45587400-45589200	Enhancers	Dnd41	blood
30	chr6:45587600-45588200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:45587600-45588400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:45587600-45588400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:45587600-45588400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:45587600-45588600	Enhancers	HMEC	breast
35	chr6:45587600-45588800	Enhancers	Primary T cells from cord blood	blood
36	chr6:45587600-45589200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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