Variant report

Variant	rs2459361
Chromosome Location	chr15:76813888-76813889
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76493051..76495991-chr15:76813493..76815400,2	MCF-7	breast:
2	chr15:76812872..76815537-chr15:76817323..76820278,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1011083	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs10152247	0.81[EUR][1000 genomes]
rs10851888	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs11072591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11072597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11072598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11072600	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072602	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072607	0.83[EUR][1000 genomes]
rs11072610	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs11072612	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs11072614	0.82[CHB][hapmap]
rs11072616	0.92[CEU][hapmap];0.86[CHB][hapmap]
rs11629888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11632222	0.84[EUR][1000 genomes]
rs11632670	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs11632765	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[YRI][hapmap]
rs11634019	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs11635463	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11637096	0.95[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs11637490	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11638767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11852777	0.83[EUR][1000 genomes]
rs11854850	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11856717	0.87[CHB][hapmap]
rs11857015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11857327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12437981	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12440511	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs12440965	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs12591100	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12898810	0.82[EUR][1000 genomes]
rs12900179	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12903874	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12904417	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs12906143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12909656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12914196	0.81[EUR][1000 genomes]
rs157783	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1603860	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1607015	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs1607017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1809875	0.82[EUR][1000 genomes]
rs2047504	0.95[CEU][hapmap];0.87[CHB][hapmap];0.81[EUR][1000 genomes]
rs2048856	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2164102	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2280306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2404734	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs2436994	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2436996	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2454450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2454451	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2454454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2461870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2461871	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2461872	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs2468130	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2468131	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2469249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs283789	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs283793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs283795	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs28895952	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2957614	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs34103231	0.82[EUR][1000 genomes]
rs3765115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs437131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4886493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4886495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4886798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4886800	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4886805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4886816	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886819	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[EUR][1000 genomes]
rs56246286	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57682236	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62026889	0.83[EUR][1000 genomes]
rs62026898	0.81[EUR][1000 genomes]
rs62028380	0.82[EUR][1000 genomes]
rs62028406	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62028423	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62028434	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7165053	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[YRI][hapmap]
rs7181506	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs744336	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8029283	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8037847	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs908817	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs965818	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv1053924	chr15:76803849-77089079	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv471254	chr15:76811390-76978139	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2459361	ZNF291	cis	lesional skin	skin_eQTL
rs2459361	SCAPER	cis	Adipose Subcutaneous	GTEx
rs2459361	SCAPER	cis	lung	GTEx
rs2459361	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs2459361	SCAPER	cis	Esophagus Mucosa	GTEx
rs2459361	ISL2	cis	Whole Blood	GTEx
rs2459361	ZNF291	cis	uninvolved skin	skin_eQTL
rs2459361	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs2459361	SCAPER	cis	Esophagus Muscularis	GTEx
rs2459361	SCAPER	cis	Nerve Tibial	GTEx
rs2459361	SCAPER	cis	Artery Tibial	GTEx
rs2459361	SCAPER	cis	Whole Blood	GTEx
rs2459361	SCAPER	cis	Thyroid	GTEx
rs2459361	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76797400-76825000	Weak transcription	Primary B cells from cord blood	blood
2	chr15:76805600-76845800	Weak transcription	Primary T cells from cord blood	blood
3	chr15:76807600-76817800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:76808000-76816200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:76808400-76825000	Weak transcription	Fetal Intestine Small	intestine
6	chr15:76808400-76825600	Weak transcription	Fetal Intestine Large	intestine
7	chr15:76811200-76825400	Weak transcription	Fetal Stomach	stomach
8	chr15:76813000-76821600	Weak transcription	Left Ventricle	heart

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