Variant report

Variant	rs4561394
Chromosome Location	chr14:104102718-104102719
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	chr14:104102424..104105194-chr14:104313193..104314702,2	MCF-7	breast:
2	chr14:104093958..104099229-chr14:104101550..104106033,7	K562	blood:

Variant related genes	Relation type
ENSG00000126214	Chromatin interaction
ENSG00000258735	Chromatin interaction
ENSG00000088808	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10047805	0.89[ASN][1000 genomes]
rs1054080	0.85[ASN][1000 genomes]
rs1078756	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11160754	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11160756	0.84[ASN][1000 genomes]
rs11850979	0.91[ASN][1000 genomes]
rs12432907	0.81[EUR][1000 genomes]
rs12432994	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12435399	0.88[ASN][1000 genomes]
rs12436795	0.83[EUR][1000 genomes]
rs12586322	0.81[EUR][1000 genomes]
rs12881418	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12889869	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12897511	0.81[ASN][1000 genomes]
rs2403203	0.88[ASN][1000 genomes]
rs2896489	0.92[ASN][1000 genomes]
rs3212103	0.81[EUR][1000 genomes]
rs3212136	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35015260	0.84[ASN][1000 genomes]
rs35140615	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35469050	0.82[EUR][1000 genomes]
rs35686878	0.95[ASN][1000 genomes]
rs35918322	0.83[ASN][1000 genomes]
rs3742465	0.89[ASN][1000 genomes]
rs3759586	0.88[ASN][1000 genomes]
rs4318144	0.82[ASN][1000 genomes]
rs4900583	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4900584	0.96[ASN][1000 genomes]
rs4900586	0.82[ASN][1000 genomes]
rs4900587	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4906340	0.89[ASN][1000 genomes]
rs4906348	0.87[ASN][1000 genomes]
rs4906349	0.97[ASN][1000 genomes]
rs4906352	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4906355	0.85[ASN][1000 genomes]
rs4906359	0.82[EUR][1000 genomes]
rs55647815	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61436277	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7145234	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7154572	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7155511	0.82[ASN][1000 genomes]
rs7156832	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs729437	0.83[ASN][1000 genomes]
rs8007903	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8007915	0.84[ASN][1000 genomes]
rs8008451	0.92[ASN][1000 genomes]
rs8012775	0.85[ASN][1000 genomes]
rs8018214	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
5	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
6	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
7	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
8	nsv902308	chr14:104087209-104211180	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	nsv1041329	chr14:104097750-104196346	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv542202	chr14:104097750-104196346	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv1048866	chr14:104100862-104195896	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4561394	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	chr14:104096600-104118000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:104097400-104103600	Weak transcription	Liver	Liver
3	chr14:104097400-104104000	Weak transcription	HepG2	liver
4	chr14:104097400-104104200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr14:104097400-104104200	Weak transcription	Aorta	Aorta
6	chr14:104097400-104104200	Weak transcription	Brain Anterior Caudate	brain
7	chr14:104097400-104104200	Weak transcription	Stomach Mucosa	stomach
8	chr14:104097400-104104200	Weak transcription	Thymus	Thymus
9	chr14:104097400-104104200	Weak transcription	NH-A	brain
10	chr14:104097400-104105000	Weak transcription	Fetal Lung	lung
11	chr14:104097400-104107400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr14:104097400-104107800	Strong transcription	Fetal Stomach	stomach
13	chr14:104097400-104117800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr14:104097400-104119400	Weak transcription	HSMMtube	muscle
15	chr14:104097400-104120000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr14:104097400-104120000	Weak transcription	HUVEC	blood vessel
17	chr14:104097400-104120200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr14:104097400-104120200	Weak transcription	Colonic Mucosa	Colon
19	chr14:104097400-104120200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr14:104097400-104120400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr14:104097400-104120400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr14:104097400-104120800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr14:104097400-104156600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr14:104097600-104106200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr14:104098200-104103000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:104098600-104119200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr14:104098600-104119800	Weak transcription	K562	blood
28	chr14:104098800-104104200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr14:104098800-104104400	Weak transcription	HMEC	breast
30	chr14:104099200-104102800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr14:104099200-104104800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr14:104099200-104120200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr14:104099400-104104000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr14:104099400-104104000	Weak transcription	Pancreas	Pancrea
35	chr14:104099400-104104200	Weak transcription	A549	lung
36	chr14:104099800-104104000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr14:104100000-104103600	Weak transcription	Fetal Brain Male	brain
38	chr14:104100000-104104000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr14:104100000-104104000	Weak transcription	Gastric	stomach
40	chr14:104100000-104104000	Weak transcription	Lung	lung
41	chr14:104100000-104104200	Weak transcription	Fetal Intestine Large	intestine
42	chr14:104100000-104119400	Weak transcription	Placenta	Placenta
43	chr14:104100200-104104000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr14:104100400-104103000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr14:104100400-104104000	Weak transcription	Fetal Muscle Leg	muscle
46	chr14:104100800-104103000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr14:104101000-104104000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr14:104101000-104104000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr14:104101000-104104000	Weak transcription	Right Atrium	heart
50	chr14:104101000-104104200	Weak transcription	Dnd41	blood

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