Variant report

Variant	rs11039390
Chromosome Location	chr11:47796295-47796296
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47796142..47797778-chr11:47800314..47803112,2	MCF-7	breast:
2	chr11:47788346..47792953-chr11:47794926..47797941,5	K562	blood:
3	chr11:47787848..47790479-chr11:47795316..47798585,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109920	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10838747	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10838748	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10838757	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039342	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039348	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11039355	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11039389	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039416	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039426	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039433	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11602339	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11602395	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11604825	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11605774	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12361031	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12364432	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12418852	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12421210	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12785833	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12787112	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12787330	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12787646	0.80[EUR][1000 genomes]
rs12798109	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12803191	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17788930	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2290850	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34128973	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34910028	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34923397	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35805829	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35902101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35985502	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4752797	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4752873	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7105282	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7120333	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7130758	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7927771	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7947730	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9909	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11039390	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs11039390	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs11039390	C1QTNF4	cis	Whole Blood	GTEx
rs11039390	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs11039390	C1QTNF4	cis	Muscle Skeletal	GTEx
rs11039390	C1QTNF4	cis	lung	GTEx
rs11039390	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs11039390	FNBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47789600-47796600	Weak transcription	Lung	lung
2	chr11:47789800-47798600	Weak transcription	Ovary	ovary
3	chr11:47790000-47797200	Weak transcription	Gastric	stomach
4	chr11:47790000-47798800	Weak transcription	Colonic Mucosa	Colon
5	chr11:47790000-47800200	Weak transcription	Psoas Muscle	Psoas
6	chr11:47790000-47800200	Weak transcription	Stomach Mucosa	stomach
7	chr11:47790000-47806800	Weak transcription	Esophagus	oesophagus
8	chr11:47790000-47837800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:47790200-47796400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:47790200-47796400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:47790200-47796400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:47790200-47796600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:47790200-47796600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:47790200-47796600	Weak transcription	Aorta	Aorta
15	chr11:47790200-47796800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:47790200-47796800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr11:47790200-47796800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:47790200-47798400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:47790200-47798600	Weak transcription	Pancreas	Pancrea
20	chr11:47790200-47798800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:47790200-47798800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr11:47790200-47798800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr11:47790200-47798800	Weak transcription	Right Ventricle	heart
24	chr11:47790200-47799000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr11:47790200-47801000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr11:47790200-47801600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr11:47790200-47805200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr11:47790200-47869200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr11:47790400-47796400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr11:47790400-47796400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:47790400-47796400	Weak transcription	Liver	Liver
32	chr11:47790400-47796400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr11:47790400-47796400	Weak transcription	Spleen	Spleen
34	chr11:47790400-47796600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:47790400-47796600	Weak transcription	Brain Germinal Matrix	brain
36	chr11:47790400-47796800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:47790400-47796800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:47790400-47796800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr11:47790400-47796800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr11:47790400-47796800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr11:47790400-47796800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr11:47790400-47796800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:47790400-47796800	Weak transcription	HMEC	breast
44	chr11:47790400-47796800	Weak transcription	Osteobl	bone
45	chr11:47790400-47797000	Weak transcription	Brain Anterior Caudate	brain
46	chr11:47790400-47797200	Weak transcription	Brain Hippocampus Middle	brain
47	chr11:47790400-47797200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr11:47790400-47798400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr11:47790400-47798400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr11:47790400-47798600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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