Variant report

Variant	rs13393385
Chromosome Location	chr2:134382097-134382098
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10165706	0.84[ASN][1000 genomes]
rs10165896	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169733	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171394	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10177415	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10185005	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185520	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10192051	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193288	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193374	0.93[ASN][1000 genomes]
rs10193580	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206506	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328892	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391014	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404176	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404397	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13407575	1.00[ASN][1000 genomes]
rs13409971	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13412577	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416986	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13419634	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425366	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13429974	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430360	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430590	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431505	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431618	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16827735	0.93[ASN][1000 genomes]
rs1901428	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1901429	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1901432	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1901433	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1901449	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1993136	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993137	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084808	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084809	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278851	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28478058	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28514481	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55646124	0.93[ASN][1000 genomes]
rs57451360	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58763272	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59085210	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60598686	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177769	0.93[ASN][1000 genomes]
rs62179347	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62180296	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62180299	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62180300	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62180302	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62180303	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6730046	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733088	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748388	0.94[EUR][1000 genomes]
rs67792617	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72843232	0.93[ASN][1000 genomes]
rs7422753	1.00[EUR][1000 genomes];1.00[ASN][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	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv516644	chr2:134301130-134391214	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv431713	chr2:134316522-134413604	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1013713	chr2:134322236-134644574	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv535931	chr2:134322236-134644574	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv2934	chr2:134368478-134412454	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv998920	chr2:134382097-134424640	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13393385	CHKA	trans	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134368000-134389800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:134377600-134385200	Weak transcription	Brain Substantia Nigra	brain
3	chr2:134381200-134383200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:134382000-134382200	Enhancers	Brain Angular Gyrus	brain
5	chr2:134382000-134382400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:134382000-134382400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:134382000-134382600	Enhancers	NHEK	skin

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