Variant report

Variant	rs60129254
Chromosome Location	chr9:93750796-93750797
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	chr9:93749370..93751733-chr9:93905841..93908265,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10123625	1.00[EUR][1000 genomes]
rs10512204	1.00[EUR][1000 genomes]
rs10991749	1.00[EUR][1000 genomes]
rs1460828	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1542478	1.00[EUR][1000 genomes]
rs1585456	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1585457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1585458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1585459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16907076	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16907078	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16907083	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16907088	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16907095	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16907097	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16907114	1.00[EUR][1000 genomes]
rs16907129	1.00[EUR][1000 genomes]
rs1841446	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28406163	1.00[EUR][1000 genomes]
rs28498576	1.00[EUR][1000 genomes]
rs28508244	0.83[ASN][1000 genomes]
rs28548848	1.00[EUR][1000 genomes]
rs28629371	1.00[EUR][1000 genomes]
rs28720686	1.00[EUR][1000 genomes]
rs296729	0.98[ASN][1000 genomes]
rs4991707	1.00[EUR][1000 genomes]
rs55796701	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55837511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56046303	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56099287	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56215441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56286690	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56748053	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57191437	0.80[AFR][1000 genomes]
rs57600683	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57756037	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57874603	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58087771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58145618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58848158	1.00[EUR][1000 genomes]
rs58968598	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59262734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59306422	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59874266	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60691320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60805834	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61300432	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61647505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479324	1.00[EUR][1000 genomes]
rs6479326	1.00[EUR][1000 genomes]
rs6479327	1.00[EUR][1000 genomes]
rs7020346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024221	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025659	1.00[EUR][1000 genomes]
rs7025935	1.00[EUR][1000 genomes]
rs7032345	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7034744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039162	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039179	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039199	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7042483	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7046222	0.96[AFR][1000 genomes]
rs7047670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73492505	0.82[AFR][1000 genomes]
rs73492518	0.89[AFR][1000 genomes]
rs73492522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73492530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73492532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73492542	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73492544	0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73492545	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73492551	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73505587	1.00[EUR][1000 genomes]
rs73653521	0.97[AFR][1000 genomes]
rs73653522	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73653527	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs751279	1.00[EUR][1000 genomes]
rs753789	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs753790	1.00[EUR][1000 genomes]
rs753791	1.00[EUR][1000 genomes]
rs7852422	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7854507	1.00[AFR][1000 genomes]
rs7854907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7856489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7856691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859976	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870440	1.00[EUR][1000 genomes]
rs7873869	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93747000-93751000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:93747600-93750800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr9:93747600-93751000	Enhancers	HMEC	breast
4	chr9:93747600-93751200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:93748200-93750800	Enhancers	NHEK	skin
6	chr9:93748200-93753800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:93748200-93753800	Weak transcription	Hela-S3	cervix
8	chr9:93748800-93754000	Weak transcription	HUVEC	blood vessel
9	chr9:93749800-93751000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:93749800-93751400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:93750200-93751000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:93750400-93750800	Enhancers	NHLF	lung
13	chr9:93750400-93751000	Enhancers	NHDF-Ad	bronchial
14	chr9:93750600-93751000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:93750600-93753800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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