Variant report

Variant	rs11039467
Chromosome Location	chr11:47965961-47965962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47931798..47934604-chr11:47964114..47966502,2	K562	blood:
2	chr11:47964794..47968609-chr11:48000698..48003518,3	MCF-7	breast:
3	chr11:47882484..47885060-chr11:47964831..47967242,2	K562	blood:
4	chr11:47964249..47967260-chr11:47967441..47970649,3	K562	blood:
5	chr11:47964759..47967260-chr11:47968299..47969907,3	K562	blood:
6	chr11:47964394..47966332-chr11:47982936..47984660,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149177	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11039464	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1997308	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2170815	0.83[JPT][hapmap]
rs6485795	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes]
rs7950674	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv897326	chr11:47891334-48035474	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11039467	C1QTNF4	cis	multi-tissue	Pritchard

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47950800-47971800	Weak transcription	Fetal Thymus	thymus
2	chr11:47954400-47968200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr11:47956800-47970200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr11:47959800-47968800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:47960000-47966000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr11:47960000-47967600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr11:47960000-47967800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:47960000-47967800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:47960000-47972400	Weak transcription	Lung	lung
10	chr11:47964000-47968400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr11:47964000-47968400	Weak transcription	GM12878-XiMat	blood
12	chr11:47964000-47972200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:47964200-47968400	Weak transcription	Placenta	Placenta
14	chr11:47964400-47967400	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr11:47964400-47967400	Weak transcription	Primary B cells from cord blood	blood
16	chr11:47964400-47967400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr11:47964400-47968800	Weak transcription	Right Atrium	heart
18	chr11:47964600-47968600	Weak transcription	Liver	Liver
19	chr11:47965400-47966000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr11:47965400-47966600	Flanking Active TSS	K562	blood
21	chr11:47965600-47966000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:47965600-47966200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:47965600-47966200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:47965600-47966200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr11:47965600-47966200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:47965600-47966200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr11:47965600-47966200	Enhancers	Placenta Amnion	Placenta Amnion
28	chr11:47965600-47966200	Flanking Active TSS	Hela-S3	cervix
29	chr11:47965600-47966400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr11:47965600-47966400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr11:47965600-47966400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr11:47965600-47966400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr11:47965600-47966400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr11:47965600-47966400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:47965600-47966600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr11:47965600-47966600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:47965600-47966600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr11:47965600-47966600	Enhancers	HUVEC	blood vessel
39	chr11:47965600-47966600	Enhancers	NH-A	brain
40	chr11:47965800-47966000	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr11:47965800-47966000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
42	chr11:47965800-47966000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr11:47965800-47966000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:47965800-47966200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
45	chr11:47965800-47966200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:47965800-47966200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr11:47965800-47966200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr11:47965800-47966200	Enhancers	Stomach Mucosa	stomach
49	chr11:47965800-47966400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:47965800-47966400	Weak transcription	Brain Inferior Temporal Lobe	brain

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