Variant report

Variant	rs12589494
Chromosome Location	chr14:104049793-104049794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:104047041..104049916-chr14:104095707..104097301,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11625397	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12897511	0.84[ASN][1000 genomes]
rs2296483	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4318144	0.83[ASN][1000 genomes]
rs4906341	0.81[AMR][1000 genomes]
rs57202218	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58601596	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7142016	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7155511	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs752624	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8007489	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs942862	0.82[EUR][1000 genomes]
rs9652403	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv902297	chr14:103956182-104061646	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902298	chr14:103959289-104061646	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS 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 lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv902299	chr14:103967504-104061646	Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	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
7	nsv902304	chr14:103979953-104061646	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv902305	chr14:103979953-104073551	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12589494	BAG5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104030800-104073200	Weak transcription	Small Intestine	intestine
2	chr14:104035400-104060400	Weak transcription	Fetal Brain Male	brain
3	chr14:104038800-104051000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr14:104041000-104059600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr14:104041000-104063200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr14:104041600-104056200	Weak transcription	K562	blood
7	chr14:104041600-104056400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr14:104041800-104052600	Weak transcription	Psoas Muscle	Psoas
9	chr14:104041800-104059600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr14:104041800-104060600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr14:104042200-104057200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr14:104043400-104051200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:104043400-104051200	Strong transcription	Fetal Intestine Large	intestine
14	chr14:104043400-104052000	Strong transcription	Fetal Intestine Small	intestine
15	chr14:104043400-104056600	Weak transcription	Fetal Heart	heart
16	chr14:104043800-104050800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr14:104043800-104051400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr14:104043800-104051600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr14:104043800-104051600	Strong transcription	Fetal Muscle Leg	muscle
20	chr14:104043800-104055400	Weak transcription	Brain Angular Gyrus	brain
21	chr14:104043800-104058200	Strong transcription	Fetal Stomach	stomach
22	chr14:104043800-104059600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr14:104043800-104060200	Weak transcription	Stomach Mucosa	stomach
24	chr14:104044000-104055000	Weak transcription	Colon Smooth Muscle	Colon
25	chr14:104044000-104056600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr14:104044600-104051000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr14:104045200-104050000	Weak transcription	HSMMtube	muscle
28	chr14:104045200-104059600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr14:104045400-104050800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr14:104045400-104054600	Weak transcription	Ovary	ovary
31	chr14:104045400-104055200	Weak transcription	A549	lung
32	chr14:104045600-104050000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr14:104045600-104050400	Weak transcription	HepG2	liver
34	chr14:104045600-104054600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr14:104045600-104054800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr14:104045600-104054800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr14:104045600-104055200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr14:104045600-104055200	Weak transcription	Brain Hippocampus Middle	brain
39	chr14:104045600-104055400	Weak transcription	Left Ventricle	heart
40	chr14:104045600-104055400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr14:104045600-104057200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr14:104045600-104057200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr14:104045600-104059400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr14:104045600-104060000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr14:104045600-104060000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr14:104045600-104060000	Weak transcription	Fetal Kidney	kidney
47	chr14:104045600-104060400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr14:104045600-104060600	Weak transcription	NHDF-Ad	bronchial
49	chr14:104045600-104067200	Weak transcription	Primary B cells from cord blood	blood
50	chr14:104045800-104055000	Weak transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links