Variant report

Variant	rs10177576
Chromosome Location	chr2:114533088-114533089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:114532490..114535142-chr2:114535239..114537247,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10167730	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10172842	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10179657	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10209098	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10209330	1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10496453	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11123206	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11123207	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11686297	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11694130	1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12613159	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12711788	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375332	0.88[EUR][1000 genomes]
rs17040397	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2122097	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290108	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs2305255	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2442136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2595152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2687623	0.86[ASN][1000 genomes]
rs2687626	0.85[ASN][1000 genomes]
rs2687627	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2687628	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2687630	0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28451366	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2900744	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34332133	0.84[ASN][1000 genomes]
rs35734534	0.85[ASN][1000 genomes]
rs3816384	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs3890789	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4848343	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4848345	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4848349	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4848350	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4849270	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4849275	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4849277	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4849278	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4849279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6711542	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7560480	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7577893	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7600228	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
2	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv2883	chr2:114507889-114535199	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv961341	chr2:114532909-114534569	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10177576	RPL23AP7	cis	Artery Aorta	GTEx
rs10177576	RPL23AP7	cis	Muscle Skeletal	GTEx
rs10177576	RPL23AP7	cis	Whole Blood	GTEx
rs10177576	RPL23AP7	cis	Nerve Tibial	GTEx
rs10177576	RPL23AP7	cis	lung	GTEx
rs10177576	RPL23AP7	cis	Esophagus Muscularis	GTEx
rs10177576	DDX11L2	cis	Whole Blood	GTEx
rs10177576	SLC35F5	Cis_1M	lymphoblastoid	RTeQTL
rs10177576	RPL23AP7	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114529800-114534600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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