Variant report

Variant	rs7945473
Chromosome Location	chr11:47589707-47589708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47586403..47589804-chr11:47615450..47617603,3	MCF-7	breast:
2	chr11:47586895..47590126-chr11:47609798..47613644,4	MCF-7	breast:
3	chr11:47571923..47578059-chr11:47583779..47591283,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149187	Chromatin interaction
ENSG00000172247	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1064608	0.81[EUR][1000 genomes]
rs10838724	0.80[ASN][1000 genomes]
rs11039307	0.88[ASN][1000 genomes]
rs11039308	0.83[ASN][1000 genomes]
rs11605348	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12363232	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12419692	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12798028	0.91[ASN][1000 genomes]
rs12798346	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12799623	0.83[EUR][1000 genomes]
rs2030166	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3817335	0.81[EUR][1000 genomes]
rs56400411	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66749409	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7928842	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers 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 miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription 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	41 gene(s)	inside rSNPs	diseases
3	nsv314	chr11:47561564-47606256	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv825872	chr11:47565425-47660330	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7945473	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs7945473	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs7945473	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs7945473	C1QTNF4	cis	Muscle Skeletal	GTEx
rs7945473	C1QTNF4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47587800-47591400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:47588000-47590000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:47588000-47590000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr11:47588000-47590400	Weak transcription	Brain Germinal Matrix	brain
5	chr11:47588000-47591200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:47588000-47591200	Weak transcription	Aorta	Aorta
7	chr11:47588000-47591200	Weak transcription	Left Ventricle	heart
8	chr11:47588000-47591200	Weak transcription	Lung	lung
9	chr11:47588000-47591200	Weak transcription	Ovary	ovary
10	chr11:47588000-47591200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr11:47588000-47592200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr11:47588000-47592800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:47588000-47592800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:47588000-47592800	Weak transcription	Brain Substantia Nigra	brain
15	chr11:47588000-47593000	Weak transcription	Gastric	stomach
16	chr11:47588000-47593000	Weak transcription	Pancreas	Pancrea
17	chr11:47588000-47593600	Weak transcription	Psoas Muscle	Psoas
18	chr11:47588000-47594000	Weak transcription	Colonic Mucosa	Colon
19	chr11:47588000-47594200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:47588000-47594200	Weak transcription	Esophagus	oesophagus
21	chr11:47588000-47594400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr11:47588000-47594600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:47588000-47599800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr11:47588000-47600000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr11:47588200-47589800	Weak transcription	Fetal Thymus	thymus
26	chr11:47588200-47590000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr11:47588200-47590000	Weak transcription	Fetal Brain Female	brain
28	chr11:47588200-47590600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr11:47588200-47591000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr11:47588200-47591000	Weak transcription	NH-A	brain
31	chr11:47588200-47591200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr11:47588200-47591200	Weak transcription	HSMM	muscle
33	chr11:47588200-47591200	Weak transcription	HSMMtube	muscle
34	chr11:47588200-47592400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr11:47588200-47592600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:47588200-47594200	Weak transcription	Right Ventricle	heart
37	chr11:47588200-47594800	Weak transcription	Small Intestine	intestine
38	chr11:47588400-47589800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr11:47588400-47589800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr11:47588400-47589800	Weak transcription	Fetal Muscle Leg	muscle
41	chr11:47588400-47590000	Weak transcription	Fetal Intestine Large	intestine
42	chr11:47588400-47590000	Weak transcription	Fetal Lung	lung
43	chr11:47588400-47590000	Weak transcription	Placenta	Placenta
44	chr11:47588400-47590000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr11:47588400-47591000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr11:47588400-47591000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr11:47588400-47591000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:47588400-47591000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr11:47588400-47591000	Weak transcription	Primary T cells from cord blood	blood
50	chr11:47588400-47591000	Weak transcription	Brain Angular Gyrus	brain

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