Variant report

Variant	rs56017123
Chromosome Location	chr14:104075277-104075278
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:104027231..104029989-chr14:104073451..104075622,2	MCF-7	breast:
2	chr14:104071968..104075598-chr14:104093991..104095637,3	MCF-7	breast:
3	chr14:104064278..104066536-chr14:104074271..104076591,2	MCF-7	breast:
4	chr14:104073010..104076125-chr14:104181634..104184420,3	MCF-7	breast:
5	chr14:104074469..104076421-chr14:104076600..104079246,2	K562	blood:
6	chr14:104033774..104035610-chr14:104074233..104076261,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126214	Chromatin interaction
ENSG00000256053	Chromatin interaction
ENSG00000100711	Chromatin interaction
ENSG00000166170	Chromatin interaction
ENSG00000126215	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10134399	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10140410	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10143293	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10145755	0.83[AFR][1000 genomes]
rs10149249	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11621777	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11624505	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11626658	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11849259	0.83[AFR][1000 genomes]
rs2274268	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2274269	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28513222	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28514618	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28660416	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28744517	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3783404	0.83[AFR][1000 genomes]
rs55864158	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55885592	0.85[AFR][1000 genomes]
rs56660916	0.85[AFR][1000 genomes]
rs57447494	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58133129	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59217746	0.84[ASN][1000 genomes]
rs59281218	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60802358	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61996716	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61996717	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61996721	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68087451	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7142883	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7154587	0.88[EUR][1000 genomes]
rs7154948	0.89[EUR][1000 genomes]
rs7693	0.89[EUR][1000 genomes]
rs8003090	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8018979	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs942863	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56017123	BAG5	Cis_1M	lymphoblastoid	RTeQTL
rs56017123	BAG5	cis	multi-tissue	Pritchard
rs56017123	APOPT1	cis	Muscle Skeletal	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104060200-104090200	Weak transcription	Pancreas	Pancrea
2	chr14:104074400-104075400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr14:104074400-104075800	Bivalent Enhancer	Fetal Muscle Leg	muscle
4	chr14:104074400-104075800	Enhancers	HSMMtube	muscle
5	chr14:104074600-104077600	Weak transcription	Brain Angular Gyrus	brain
6	chr14:104074800-104075400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
7	chr14:104075000-104076800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:104075000-104077600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr14:104075200-104075400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
10	chr14:104075200-104075800	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr14:104075200-104076200	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links