Variant report

Variant	rs12905477
Chromosome Location	chr15:49645646-49645647
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10519224	0.92[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10519225	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10851478	1.00[YRI][hapmap]
rs11070706	1.00[YRI][hapmap]
rs11853969	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11854039	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11854557	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11855798	0.92[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11857515	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11858411	1.00[YRI][hapmap]
rs11858814	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12232355	1.00[YRI][hapmap]
rs12591300	0.83[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs12592508	0.92[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs12899422	0.92[AFR][1000 genomes]
rs12901353	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12901929	0.92[CEU][hapmap];0.80[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12902096	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902271	0.84[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12905094	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12905203	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs12908624	1.00[YRI][hapmap]
rs12914876	0.88[AFR][1000 genomes]
rs12916839	0.80[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs17402115	1.00[YRI][hapmap]
rs17435932	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17472989	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17478694	0.88[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs17478785	0.88[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1911612	1.00[YRI][hapmap]
rs1961393	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2289389	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs34562714	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs34748066	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36023246	1.00[AFR][1000 genomes]
rs36100631	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4389093	0.88[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap]
rs4436732	0.84[AFR][1000 genomes]
rs4547278	0.84[AFR][1000 genomes]
rs4774538	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4775806	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4775808	0.96[AFR][1000 genomes]
rs55979115	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62009834	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62009977	0.84[AFR][1000 genomes]
rs6493372	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs7180168	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7497335	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8029687	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs8033184	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8043493	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9920722	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12905477	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49623200-49646000	Weak transcription	Left Ventricle	heart
2	chr15:49623400-49647600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:49644600-49646600	Weak transcription	Aorta	Aorta

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