Variant report

Variant	rs6459115
Chromosome Location	chr6:55784278-55784279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10498808	0.99[ASN][1000 genomes]
rs12198217	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12199367	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12209768	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1447127	0.91[ASN][1000 genomes]
rs1447128	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1447132	0.88[EUR][1000 genomes]
rs1562407	0.94[ASN][1000 genomes]
rs1562408	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16887395	0.97[ASN][1000 genomes]
rs1838946	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1868031	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2021803	0.81[CHD][hapmap]
rs2028956	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2044542	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2044543	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2056424	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3807016	0.81[CHD][hapmap]
rs4560651	0.90[ASN][1000 genomes]
rs4574618	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4599631	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715570	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4715571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6459111	0.84[ASN][1000 genomes]
rs6459112	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6459113	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6459116	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6459118	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6912214	0.82[CHD][hapmap]
rs6925961	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6926331	0.89[EUR][1000 genomes]
rs6932412	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72870626	0.89[EUR][1000 genomes]
rs7752119	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7755388	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7755393	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7758580	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7770068	0.83[EUR][1000 genomes]
rs895641	0.97[ASN][1000 genomes]
rs895642	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs895643	0.97[ASN][1000 genomes]
rs9296807	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9296809	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9296810	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464303	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9475467	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9475469	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9475471	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9475472	0.97[ASN][1000 genomes]
rs9475473	0.97[ASN][1000 genomes]
rs9475477	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9475480	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs978930	0.82[CHD][hapmap]
rs9885708	0.83[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1024174	chr6:55713889-55829936	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1029301	chr6:55713889-55834480	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv830665	chr6:55755560-55920219	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6459115	C6orf142	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55780800-55784600	Enhancers	Hela-S3	cervix
2	chr6:55780800-55784600	Enhancers	HSMM	muscle
3	chr6:55780800-55785000	Enhancers	Muscle Satellite Cultured Cells	--
4	chr6:55781200-55784400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:55782400-55784400	Weak transcription	HMEC	breast
6	chr6:55783400-55789800	Weak transcription	NHEK	skin
7	chr6:55783600-55785000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:55783800-55784800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:55784200-55785000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:55784200-55785000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:55784200-55789600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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