Variant report

Variant	rs11039355
Chromosome Location	chr11:47737501-47737502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:47736502-47738601	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr11:47736524-47737628	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47734421..47738084-chr11:47868728..47871724,4	K562	blood:
2	chr11:47662579..47666117-chr11:47735408..47738256,8	MCF-7	breast:
3	chr11:47662583..47667763-chr11:47735291..47739208,6	MCF-7	breast:
4	chr11:47733919..47739426-chr11:47787626..47790588,5	MCF-7	breast:
5	chr11:47735300..47737622-chr11:47868024..47869979,2	MCF-7	breast:
6	chr11:47736234..47739669-chr11:47788606..47790744,3	MCF-7	breast:

No data

Variant related genes	Relation type
AGBL2	TF binding region
ENSG00000109919	Chromatin interaction
ENSG00000109920	Chromatin interaction
ENSG00000030066	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1064608	0.80[ASN][1000 genomes]
rs10838738	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10838747	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10838748	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10838757	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039308	0.81[ASN][1000 genomes]
rs11039342	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039348	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039389	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039390	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11039391	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11039416	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11039426	0.82[ASN][1000 genomes]
rs11039433	0.81[AMR][1000 genomes]
rs11602339	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11602395	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11604825	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11605774	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11823949	0.82[ASN][1000 genomes]
rs12361031	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12363232	0.81[AMR][1000 genomes]
rs12418852	0.81[ASN][1000 genomes]
rs12419692	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12421210	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12785833	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12787112	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12787330	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12787646	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12794570	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12798109	0.81[AMR][1000 genomes]
rs12803191	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17788930	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2290850	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34128973	0.82[ASN][1000 genomes]
rs34910028	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34923397	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35805829	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35902101	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35985502	0.82[ASN][1000 genomes]
rs3817334	0.81[ASN][1000 genomes]
rs3817335	0.81[ASN][1000 genomes]
rs4752797	0.81[AMR][1000 genomes]
rs4752856	0.81[ASN][1000 genomes]
rs4752857	0.81[ASN][1000 genomes]
rs4752873	0.82[ASN][1000 genomes]
rs59360790	0.83[ASN][1000 genomes]
rs7120333	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7130758	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7927771	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7947730	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9909	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469858	chr11:47647515-47837172	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv832143	chr11:47700808-47883540	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11039355	C1QTNF4	cis	lung	GTEx
rs11039355	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs11039355	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs11039355	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs11039355	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs11039355	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs11039355	C1QTNF4	cis	Muscle Skeletal	GTEx
rs11039355	C1QTNF4	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47732400-47737600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:47736800-47737800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:47736800-47752400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:47737000-47738000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:47737000-47738400	Weak transcription	Lung	lung
6	chr11:47737000-47739200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:47737000-47786200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:47737200-47737600	Weak transcription	Hela-S3	cervix
9	chr11:47737200-47737800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr11:47737200-47737800	Weak transcription	Placenta	Placenta
11	chr11:47737200-47737800	Weak transcription	Fetal Thymus	thymus
12	chr11:47737200-47738000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:47737200-47738000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:47737200-47738000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr11:47737200-47738000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr11:47737200-47738000	Weak transcription	HSMMtube	muscle
17	chr11:47737200-47738000	Weak transcription	NHDF-Ad	bronchial
18	chr11:47737200-47738200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:47737200-47738200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr11:47737200-47738200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr11:47737200-47738200	Weak transcription	Adipose Nuclei	Adipose
22	chr11:47737200-47738200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr11:47737200-47738200	Weak transcription	Left Ventricle	heart
24	chr11:47737200-47738200	Weak transcription	NHLF	lung
25	chr11:47737200-47738400	Weak transcription	Fetal Muscle Leg	muscle
26	chr11:47737200-47738400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr11:47737200-47738400	Weak transcription	Right Ventricle	heart
28	chr11:47737200-47738400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr11:47737200-47738400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr11:47737200-47738400	Weak transcription	K562	blood
31	chr11:47737200-47739600	Weak transcription	Small Intestine	intestine
32	chr11:47737200-47739800	Weak transcription	Ovary	ovary
33	chr11:47737200-47740000	Weak transcription	Colonic Mucosa	Colon
34	chr11:47737200-47740200	Weak transcription	Fetal Kidney	kidney
35	chr11:47737200-47740400	Weak transcription	Brain Angular Gyrus	brain
36	chr11:47737200-47740400	Weak transcription	Pancreas	Pancrea
37	chr11:47737200-47740400	Weak transcription	Spleen	Spleen
38	chr11:47737200-47740600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:47737200-47740600	Weak transcription	Esophagus	oesophagus
40	chr11:47737200-47740800	Weak transcription	Fetal Brain Male	brain
41	chr11:47737200-47742600	Weak transcription	Gastric	stomach
42	chr11:47737200-47743000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr11:47737200-47743000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:47737200-47743000	Weak transcription	Fetal Heart	heart
45	chr11:47737200-47744000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr11:47737200-47745200	Weak transcription	Aorta	Aorta
47	chr11:47737200-47745200	Weak transcription	Psoas Muscle	Psoas
48	chr11:47737200-47745600	Weak transcription	Stomach Mucosa	stomach
49	chr11:47737200-47747400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr11:47737200-47748000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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