Variant report

Variant	rs11039389
Chromosome Location	chr11:47796062-47796063
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	chr11:47788346..47792953-chr11:47794926..47797941,5	K562	blood:
2	chr11:47787848..47790479-chr11:47795316..47798585,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109920	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10838747	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10838748	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10838757	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039342	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11039348	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11039355	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039390	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039391	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039416	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039426	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039433	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11602339	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11602395	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11604825	0.80[ASN][1000 genomes]
rs11605774	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12361031	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12364432	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12418852	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12421210	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12785833	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12787112	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12787330	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12798109	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12803191	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17788930	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2290850	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34128973	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34910028	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34923397	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35805829	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35902101	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35985502	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4752797	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4752873	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7105282	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7120333	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7130758	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7927771	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7947730	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9909	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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
rs11039389	C1QTNF4	cis	Muscle Skeletal	GTEx
rs11039389	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs11039389	C1QTNF4	cis	Whole Blood	GTEx
rs11039389	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs11039389	C1QTNF4	cis	Artery Tibial	GTEx
rs11039389	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs11039389	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs11039389	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx

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	chr11:47790200-47796200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr11:47790200-47796200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr11:47790200-47796200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr11:47790200-47796200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr11:47790200-47796200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:47790200-47796200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:47790200-47796400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:47790200-47796400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:47790200-47796400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr11:47790200-47796600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:47790200-47796600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr11:47790200-47796600	Weak transcription	Aorta	Aorta
21	chr11:47790200-47796800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:47790200-47796800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:47790200-47796800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr11:47790200-47798400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr11:47790200-47798600	Weak transcription	Pancreas	Pancrea
26	chr11:47790200-47798800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:47790200-47798800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr11:47790200-47798800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr11:47790200-47798800	Weak transcription	Right Ventricle	heart
30	chr11:47790200-47799000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr11:47790200-47801000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr11:47790200-47801600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr11:47790200-47805200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr11:47790200-47869200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr11:47790400-47796200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:47790400-47796200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr11:47790400-47796200	Weak transcription	Primary T cells from cord blood	blood
38	chr11:47790400-47796200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr11:47790400-47796200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:47790400-47796200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:47790400-47796200	Weak transcription	Fetal Brain Female	brain
42	chr11:47790400-47796200	Weak transcription	Placenta	Placenta
43	chr11:47790400-47796200	Weak transcription	Fetal Stomach	stomach
44	chr11:47790400-47796200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr11:47790400-47796200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr11:47790400-47796200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr11:47790400-47796200	Weak transcription	A549	lung
48	chr11:47790400-47796200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr11:47790400-47796200	Weak transcription	NHEK	skin
50	chr11:47790400-47796200	Weak transcription	NHLF	lung

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