Variant report

Variant	rs2851520
Chromosome Location	chr7:69054756-69054757
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1003404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10260553	0.97[ASN][1000 genomes]
rs10487947	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12670658	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12698804	0.88[TSI][hapmap]
rs1548748	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17140651	0.82[ASN][1000 genomes]
rs17140890	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1990444	0.97[ASN][1000 genomes]
rs210602	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs210605	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2215354	0.92[ASN][1000 genomes]
rs2533436	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2533437	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2851486	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2851493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851519	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34201872	0.80[AMR][1000 genomes]
rs34387293	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34650051	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34701787	0.84[ASN][1000 genomes]
rs34824391	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35241473	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35351867	0.80[AMR][1000 genomes]
rs41848	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs41854	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs41857	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4717522	0.97[ASN][1000 genomes]
rs548556	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs569334	0.97[ASN][1000 genomes]
rs628885	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs633927	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6953849	0.85[ASN][1000 genomes]
rs917617	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023885	chr7:68894896-69158290	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv538915	chr7:68894896-69158290	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv916011	chr7:68942155-69330800	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv428169	chr7:69021482-69196743	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv5783	chr7:69048608-69066760	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2851520	STAG3L4	cis	cerebellum	SCAN
rs2851520	SBDS	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69053000-69054800	Enhancers	Brain Hippocampus Middle	brain
2	chr7:69053000-69055000	Enhancers	Brain Cingulate Gyrus	brain
3	chr7:69053600-69054800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr7:69054200-69054800	Enhancers	Brain Substantia Nigra	brain
5	chr7:69054400-69056000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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