Variant report

Variant	rs3825566
Chromosome Location	chr14:103852725-103852726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr14:103840813..103842948-chr14:103850567..103853142,2	MCF-7	breast:
2	chr14:103851236..103854697-chr14:103993929..103996210,3	MCF-7	breast:
3	chr14:103804940..103815889-chr14:103850459..103863829,28	K562	blood:
4	chr14:103794753..103806137-chr14:103849038..103864103,36	MCF-7	breast:
5	chr14:103806698..103810659-chr14:103850742..103855221,6	MCF-7	breast:
6	chr14:103799041..103818802-chr14:103836567..103862153,82	K562	blood:
7	chr14:103797262..103804754-chr14:103849003..103864058,49	MCF-7	breast:
8	chr14:103798959..103802101-chr14:103850214..103852987,6	K562	blood:
9	chr14:103570168..103572327-chr14:103851557..103853448,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000166166	Chromatin interaction
ENSG00000205436	Chromatin interaction
ENSG00000260285	Chromatin interaction
ENSG00000272533	Chromatin interaction
ENSG00000243904	Chromatin interaction
ENSG00000259775	Chromatin interaction
ENSG00000100664	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10134580	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1013650	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10139279	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10141120	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10141388	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10141433	0.83[EUR][1000 genomes]
rs10143247	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10145793	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10150072	0.81[EUR][1000 genomes]
rs1028613	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11621510	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622356	0.81[ASN][1000 genomes]
rs11623869	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11624367	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11626483	0.81[ASN][1000 genomes]
rs11628213	0.84[EUR][1000 genomes]
rs11628969	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12879085	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12888077	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12889639	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12890750	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12898029	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17617941	0.84[EUR][1000 genomes]
rs17679475	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1951392	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1961600	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989565	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010281	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273700	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2273703	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2403180	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28369539	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28444993	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28496120	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28583452	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28626081	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34216351	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3742458	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3759579	0.81[ASN][1000 genomes]
rs3783394	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3783395	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3783402	0.82[EUR][1000 genomes]
rs4900572	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4906321	0.82[EUR][1000 genomes]
rs56365443	0.84[EUR][1000 genomes]
rs62006268	0.84[EUR][1000 genomes]
rs62007681	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62007683	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62007684	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62007686	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62007687	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62007718	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62007719	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6575983	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6575984	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140564	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7145113	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7146506	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7150317	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7152202	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7154246	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7155014	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7156150	0.82[EUR][1000 genomes]
rs7158144	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7158822	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7160208	0.84[EUR][1000 genomes]
rs7160366	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72708854	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72708874	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72708893	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8013101	0.84[EUR][1000 genomes]
rs8015918	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8019578	0.81[EUR][1000 genomes]
rs9671911	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042714	chr14:103085298-103860730	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1049747	chr14:103126148-103955984	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
3	nsv534254	chr14:103470073-104023906	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
4	nsv9168	chr14:103531729-103913306	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	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
6	nsv542200	chr14:103838939-103868007	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3825566	BAG5	cis	multi-tissue	Pritchard
rs3825566	MARK3	cis	Thyroid	GTEx
rs3825566	BAG5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:103850800-103853600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr14:103850800-103853600	Active TSS	Rectal Smooth Muscle	rectum
3	chr14:103850800-103854200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr14:103850800-103854400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr14:103851000-103853000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr14:103851000-103853000	Active TSS	Brain Anterior Caudate	brain
7	chr14:103851000-103853200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:103851000-103853200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr14:103851000-103853200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr14:103851000-103853200	Active TSS	Esophagus	oesophagus
11	chr14:103851000-103853200	Active TSS	Fetal Brain Female	brain
12	chr14:103851000-103853400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr14:103851000-103853400	Active TSS	Fetal Kidney	kidney
14	chr14:103851000-103853400	Active TSS	Osteobl	bone
15	chr14:103851000-103853600	Active TSS	H9 Cell Line	embryonic stem cell
16	chr14:103851000-103853600	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr14:103851000-103853800	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr14:103851000-103854200	Active TSS	Aorta	Aorta
19	chr14:103851000-103854200	Active TSS	HSMM	muscle
20	chr14:103851000-103855000	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr14:103851000-103855000	Active TSS	Right Atrium	heart
22	chr14:103851000-103855200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr14:103851200-103852800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr14:103851200-103852800	Active TSS	Brain Hippocampus Middle	brain
25	chr14:103851200-103853000	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr14:103851200-103853000	Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr14:103851200-103853000	Active TSS	Brain Substantia Nigra	brain
28	chr14:103851200-103853000	Active TSS	Small Intestine	intestine
29	chr14:103851200-103853200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr14:103851200-103853200	Active TSS	Fetal Heart	heart
31	chr14:103851200-103853200	Active TSS	Gastric	stomach
32	chr14:103851200-103853400	Active TSS	Colon Smooth Muscle	Colon
33	chr14:103851200-103853400	Active TSS	Fetal Stomach	stomach
34	chr14:103851200-103853400	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr14:103851200-103853600	Active TSS	H1 Cell Line	embryonic stem cell
36	chr14:103851200-103853600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr14:103851200-103853600	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr14:103851200-103853800	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr14:103851200-103853800	Active TSS	Left Ventricle	heart
40	chr14:103851200-103853800	Active TSS	Lung	lung
41	chr14:103851200-103853800	Active TSS	Psoas Muscle	Psoas
42	chr14:103851200-103853800	Active TSS	A549	lung
43	chr14:103851200-103853800	Active TSS	HSMMtube	muscle
44	chr14:103851200-103854000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr14:103851200-103854000	Active TSS	Brain Angular Gyrus	brain
46	chr14:103851200-103854000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr14:103851200-103854000	Active TSS	Ovary	ovary
48	chr14:103851200-103854000	Active TSS	Thymus	Thymus
49	chr14:103851200-103854200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr14:103851200-103854200	Active TSS	Brain Inferior Temporal Lobe	brain

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