Variant report

Variant	rs59538909
Chromosome Location	chr1:98542494-98542495
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs17117964	1.00[AMR][1000 genomes]
rs57653088	1.00[AMR][1000 genomes]
rs58243347	1.00[AMR][1000 genomes]
rs58638365	1.00[AMR][1000 genomes]
rs58639633	1.00[AMR][1000 genomes]
rs58893462	1.00[AMR][1000 genomes]
rs59037638	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59356371	1.00[AMR][1000 genomes]
rs59954273	1.00[AMR][1000 genomes]
rs60078043	1.00[AMR][1000 genomes]
rs60887083	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60911244	1.00[AMR][1000 genomes]
rs61174144	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61211497	1.00[AMR][1000 genomes]
rs61492808	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6662081	1.00[AMR][1000 genomes]
rs72963706	1.00[AMR][1000 genomes]
rs72963734	1.00[AMR][1000 genomes]
rs72963743	1.00[AMR][1000 genomes]
rs72963747	1.00[AMR][1000 genomes]
rs72963772	1.00[AMR][1000 genomes]
rs72967637	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72967645	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72967661	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72969626	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72969641	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72969655	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72969666	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72969667	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72969669	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72969673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72969678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72969696	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72969699	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72979743	1.00[AMR][1000 genomes]
rs72979754	1.00[AMR][1000 genomes]
rs72979756	1.00[AMR][1000 genomes]
rs72979762	1.00[AMR][1000 genomes]
rs72979773	1.00[AMR][1000 genomes]
rs72979780	1.00[AMR][1000 genomes]
rs72979786	1.00[AMR][1000 genomes]
rs72979788	1.00[AMR][1000 genomes]
rs72981731	1.00[AMR][1000 genomes]
rs72981733	1.00[AMR][1000 genomes]
rs72981734	1.00[AMR][1000 genomes]
rs72981735	1.00[AMR][1000 genomes]
rs72981737	1.00[AMR][1000 genomes]
rs72981745	1.00[AMR][1000 genomes]
rs72981751	1.00[AMR][1000 genomes]
rs72981754	1.00[AMR][1000 genomes]
rs72981756	1.00[AMR][1000 genomes]
rs72981760	1.00[AMR][1000 genomes]
rs72981761	1.00[AMR][1000 genomes]
rs72981763	1.00[AMR][1000 genomes]
rs72981765	1.00[AMR][1000 genomes]
rs72981766	1.00[AMR][1000 genomes]
rs72981768	1.00[AMR][1000 genomes]
rs72981774	1.00[AMR][1000 genomes]
rs74106051	1.00[AMR][1000 genomes]
rs74106378	1.00[AMR][1000 genomes]
rs7517110	1.00[AMR][1000 genomes]
rs7553077	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012958	chr1:98081528-98864746	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv871625	chr1:98165091-98564736	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1009621	chr1:98435638-98599284	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	nsv871230	chr1:98436232-98564736	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
5	nsv470729	chr1:98461443-98564736	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
6	nsv546874	chr1:98461443-98564736	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
7	nsv830736	chr1:98488491-98663726	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
8	nsv432531	chr1:98524979-98604179	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:98527800-98544200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:98530400-98542600	Weak transcription	NHDF-Ad	bronchial
3	chr1:98540800-98543600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:98540800-98549400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:98542400-98542600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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