Variant report

Variant	rs572761
Chromosome Location	chr13:54793133-54793134
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs2576139	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576140	1.00[EUR][1000 genomes]
rs2782516	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2818221	0.98[EUR][1000 genomes]
rs490751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs493274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs496180	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505155	1.00[EUR][1000 genomes]
rs524486	0.95[EUR][1000 genomes]
rs525758	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs556714	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568227	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs584860	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586049	0.91[EUR][1000 genomes]
rs593897	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596327	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs625472	0.98[EUR][1000 genomes]
rs631641	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs635395	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs651356	0.95[EUR][1000 genomes]
rs662226	1.00[EUR][1000 genomes]
rs679177	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs795636	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs795659	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9536647	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3375545	chr13:54517432-54908108	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv561701	chr13:54711276-54826104	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1051063	chr13:54777487-54997866	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv541778	chr13:54777487-54997866	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1046376	chr13:54785036-54827801	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	esv2763024	chr13:54786785-54822165	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv518338	chr13:54788842-54812498	Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	inside rSNPs	n/a
8	nsv818962	chr13:54788842-54812498	Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a
9	esv3693144	chr13:54788842-54816326	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers	lncRNA	n/a	inside rSNPs	n/a
10	nsv471132	chr13:54788842-54885744	ZNF genes & repeats Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs572761	LHX2	trans	lymphoblastoid	seeQTL
rs572761	SIRPG	trans	lymphoblastoid	seeQTL
rs572761	ELOVL5	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:54792800-54793400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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