Variant report

Variant	rs10134399
Chromosome Location	chr14:104083457-104083458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:104082385..104086992-chr14:104091546..104095529,4	MCF-7	breast:
2	chr14:104083399..104085556-chr14:104120787..104122860,2	MCF-7	breast:
3	chr14:104080580..104083497-chr14:104087946..104089834,2	K562	blood:

Variant related genes	Relation type
ENSG00000126214	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10135248	0.92[CEU][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs10140410	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10143293	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10145755	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10147049	0.83[EUR][1000 genomes]
rs10149249	0.96[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs11621777	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11624505	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11626658	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11849259	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2274268	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs2274269	0.81[EUR][1000 genomes]
rs2403205	0.83[ASW][hapmap];0.92[CEU][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs28514618	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28660416	0.82[EUR][1000 genomes]
rs28744517	0.82[EUR][1000 genomes]
rs3783404	0.92[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3915733	0.82[EUR][1000 genomes]
rs55864158	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55885592	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56017123	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56660916	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57218990	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57447494	0.81[EUR][1000 genomes]
rs58133129	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59217746	0.87[ASN][1000 genomes]
rs59281218	0.81[EUR][1000 genomes]
rs60802358	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61995780	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61996716	0.82[EUR][1000 genomes]
rs61996717	0.82[EUR][1000 genomes]
rs61996721	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6593	0.81[EUR][1000 genomes]
rs68087451	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs709400	0.83[ASW][hapmap];0.92[CEU][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs7142883	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7150141	0.92[CEU][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs7154948	0.87[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap]
rs7693	0.87[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap]
rs8003090	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8005885	0.82[AMR][1000 genomes]
rs8018979	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs861528	0.91[JPT][hapmap]
rs861531	0.92[CEU][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs861534	0.91[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs861536	0.83[ASW][hapmap];0.92[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs861538	0.81[EUR][1000 genomes]
rs861539	0.83[ASW][hapmap];0.88[CEU][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs861548	0.83[EUR][1000 genomes]
rs942863	0.87[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv832883	chr14:103927687-104120953	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv566022	chr14:104007555-104092789	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1052010	chr14:104061472-104216267	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv542201	chr14:104061472-104216267	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv456435	chr14:104061646-104198251	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
8	nsv566023	chr14:104061646-104198251	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
9	esv3490243	chr14:104083248-104099394	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
10	esv3490244	chr14:104083248-104099394	Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10134399	BAG5	Cis_1M	lymphoblastoid	RTeQTL
rs10134399	BAG5	cis	multi-tissue	Pritchard
rs10134399	APOPT1	cis	Muscle Skeletal	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104060200-104090200	Weak transcription	Pancreas	Pancrea
2	chr14:104078400-104090000	Weak transcription	Fetal Lung	lung
3	chr14:104079400-104085200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr14:104079800-104085400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr14:104080800-104085600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr14:104083200-104083600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr14:104083200-104084000	Flanking Active TSS	HepG2	liver
8	chr14:104083400-104083600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr14:104083400-104083800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin

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