Variant report

Variant	rs2461872
Chromosome Location	chr15:76777614-76777615
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11072591	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs11072597	0.84[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes]
rs11072598	0.84[CEU][hapmap];0.88[CHB][hapmap];0.84[AMR][1000 genomes]
rs11072613	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap]
rs11072614	0.84[CEU][hapmap];0.86[CHB][hapmap]
rs11629888	0.85[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes]
rs11630185	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap]
rs11632222	0.81[AMR][1000 genomes]
rs11633309	0.80[CEU][hapmap];0.86[CHB][hapmap]
rs11634019	0.84[CHB][hapmap]
rs11635463	0.80[CEU][hapmap];0.89[CHB][hapmap];0.84[AMR][1000 genomes]
rs11636612	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap]
rs11637490	0.83[AMR][1000 genomes]
rs11638767	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs11855644	0.85[CHB][hapmap]
rs11856717	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11857015	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs11857327	0.84[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes]
rs12591100	0.85[CHB][hapmap]
rs12906143	0.85[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes]
rs12909656	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs12915184	0.83[CEU][hapmap];0.86[CHB][hapmap]
rs1568083	0.85[CHB][hapmap]
rs157783	0.85[CHB][hapmap]
rs1607015	0.81[CEU][hapmap];0.89[CHB][hapmap];0.81[AMR][1000 genomes]
rs1607017	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs2280306	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs2436994	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs2454450	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs2454454	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs2459361	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs2461870	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs2461871	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs2469249	0.90[CHB][hapmap]
rs283789	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs283793	0.89[CHB][hapmap]
rs283795	0.85[CHB][hapmap]
rs2957614	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs3765115	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs437131	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs4886489	0.89[CHB][hapmap]
rs4886493	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs4886495	0.85[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes]
rs4886794	0.89[CHB][hapmap]
rs4886795	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4886798	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs4886800	0.90[CHB][hapmap]
rs4886804	0.80[CHB][hapmap];0.81[ASN][1000 genomes]
rs4886805	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes]
rs4886823	0.84[CEU][hapmap];0.86[CHB][hapmap]
rs62028423	0.83[AMR][1000 genomes]
rs62028434	0.85[AMR][1000 genomes]
rs744336	0.85[CHB][hapmap]
rs908817	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2461872	SCAPER	cis	lung	GTEx
rs2461872	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs2461872	SCAPER	cis	Thyroid	GTEx
rs2461872	SCAPER	cis	Esophagus Muscularis	GTEx
rs2461872	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs2461872	SCAPER	cis	Whole Blood	GTEx
rs2461872	SCAPER	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76725800-76812600	Weak transcription	Left Ventricle	heart
2	chr15:76763000-76795000	Weak transcription	Primary B cells from cord blood	blood

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