Variant report

Variant	rs12661124
Chromosome Location	chr6:45595551-45595552
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	chr6:45575296..45578545-chr6:45595416..45597740,3	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10080253	0.81[ASN][1000 genomes]
rs12528502	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12661055	0.85[ASN][1000 genomes]
rs12663210	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665637	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491142	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16873543	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16873550	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs16873554	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2020084	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56083876	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58129892	0.85[ASN][1000 genomes]
rs59074904	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs60540355	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60884282	0.81[ASN][1000 genomes]
rs6458449	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6458450	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6458454	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6458455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899443	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6902401	0.85[ASN][1000 genomes]
rs6916895	0.85[ASN][1000 genomes]
rs6917651	0.85[ASN][1000 genomes]
rs6934210	0.81[ASN][1000 genomes]
rs6938247	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs6938489	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6940187	0.85[ASN][1000 genomes]
rs6941971	0.82[ASN][1000 genomes]
rs73457129	0.84[AFR][1000 genomes]
rs73738527	0.82[ASN][1000 genomes]
rs73738528	0.85[ASN][1000 genomes]
rs7742335	0.85[AFR][1000 genomes]
rs7744486	0.82[ASN][1000 genomes]
rs7752200	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7758915	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7759415	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7760394	0.82[AFR][1000 genomes]
rs7763886	0.81[ASN][1000 genomes]
rs7764338	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs9296462	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9296463	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9463108	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9472518	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9472524	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9472525	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9472527	0.82[ASN][1000 genomes]
rs9472530	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472531	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9472532	0.81[ASN][1000 genomes]
rs9472534	0.87[AMR][1000 genomes];0.90[EUR][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
rs12661124	SPATA20	trans	lymphoblastoid	seeQTL
rs12661124	ENPP4	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45588400-45597800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:45588600-45601000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:45594000-45598200	Weak transcription	Ovary	ovary
4	chr6:45594200-45604400	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:45594400-45597800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:45594600-45596200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:45594600-45598400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:45594800-45597200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:45594800-45597800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:45594800-45598000	Weak transcription	NHLF	lung
11	chr6:45594800-45599200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:45595000-45597600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:45595000-45598000	Weak transcription	NHDF-Ad	bronchial
14	chr6:45595000-45607600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:45595200-45597800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:45595200-45598400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr6:45595200-45598800	Weak transcription	HMEC	breast
18	chr6:45595200-45598800	Weak transcription	NHEK	skin
19	chr6:45595400-45598200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:45595400-45598200	Weak transcription	Osteobl	bone
21	chr6:45595400-45598600	Weak transcription	Hela-S3	cervix

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