Variant report

Variant	rs66749409
Chromosome Location	chr11:47568074-47568075
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47556325..47561893-chr11:47562676..47568878,7	K562	blood:
2	chr11:47565515..47568693-chr11:47572907..47576173,5	K562	blood:
3	chr11:47557985..47562133-chr11:47565496..47569267,5	K562	blood:
4	chr11:47564735..47568693-chr11:47572355..47576179,6	K562	blood:
5	chr11:47559176..47561794-chr11:47565770..47569453,3	MCF-7	breast:
6	chr11:47543279..47546104-chr11:47567027..47568704,2	K562	blood:

Variant related genes	Relation type
ENSG00000149187	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1064608	0.84[ASN][1000 genomes]
rs10838724	0.84[ASN][1000 genomes]
rs10838738	0.84[ASN][1000 genomes]
rs11039255	0.81[ASN][1000 genomes]
rs11039307	0.92[ASN][1000 genomes]
rs11039308	0.88[ASN][1000 genomes]
rs11605348	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12363232	0.86[ASN][1000 genomes]
rs12419692	0.88[ASN][1000 genomes]
rs12787646	0.80[ASN][1000 genomes]
rs12794570	0.85[ASN][1000 genomes]
rs12798028	0.93[ASN][1000 genomes]
rs12798346	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12799623	0.83[ASN][1000 genomes]
rs1317149	0.83[ASN][1000 genomes]
rs2030166	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34958982	0.85[ASN][1000 genomes]
rs35184771	0.81[ASN][1000 genomes]
rs3817334	0.85[ASN][1000 genomes]
rs3817335	0.85[ASN][1000 genomes]
rs4752845	0.85[ASN][1000 genomes]
rs4752856	0.85[ASN][1000 genomes]
rs4752857	0.85[ASN][1000 genomes]
rs56400411	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59360790	0.80[ASN][1000 genomes]
rs7124681	0.83[ASN][1000 genomes]
rs7928842	0.87[ASN][1000 genomes]
rs7945473	0.82[EUR][1000 genomes];0.90[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	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	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs66749409	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs66749409	C1QTNF4	cis	Muscle Skeletal	GTEx
rs66749409	C1QTNF4	cis	Whole Blood	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47546000-47572400	Weak transcription	Fetal Intestine Large	intestine
2	chr11:47546400-47573400	Weak transcription	Colonic Mucosa	Colon
3	chr11:47546400-47573600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:47553000-47573200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:47554400-47572400	Weak transcription	Aorta	Aorta
6	chr11:47554800-47571600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:47554800-47572400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:47558400-47572600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr11:47559000-47571800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr11:47559600-47572600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr11:47561600-47573200	Weak transcription	Placenta	Placenta
12	chr11:47562000-47570600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:47562000-47571800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:47562000-47572600	Weak transcription	Brain Substantia Nigra	brain
15	chr11:47562200-47569000	Weak transcription	Pancreas	Pancrea
16	chr11:47562200-47571200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:47562200-47572000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:47562200-47572600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr11:47562200-47572800	Weak transcription	Fetal Kidney	kidney
20	chr11:47562400-47569200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:47562400-47572200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:47562600-47569200	Weak transcription	A549	lung
23	chr11:47562600-47569400	Weak transcription	Primary B cells from cord blood	blood
24	chr11:47562600-47570600	Weak transcription	Fetal Brain Female	brain
25	chr11:47562600-47570800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:47562600-47571600	Weak transcription	Right Atrium	heart
27	chr11:47562600-47571800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr11:47562600-47572400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:47562600-47572400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr11:47562600-47572400	Weak transcription	Right Ventricle	heart
31	chr11:47562600-47573200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr11:47562800-47568200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr11:47562800-47568200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr11:47562800-47569200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:47562800-47569200	Weak transcription	Osteobl	bone
36	chr11:47562800-47569400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:47562800-47570600	Weak transcription	Dnd41	blood
38	chr11:47562800-47571200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr11:47562800-47572200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr11:47562800-47572200	Weak transcription	NH-A	brain
41	chr11:47562800-47572200	Weak transcription	NHLF	lung
42	chr11:47562800-47572400	Weak transcription	Stomach Mucosa	stomach
43	chr11:47562800-47572400	Weak transcription	NHDF-Ad	bronchial
44	chr11:47563000-47568600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr11:47563000-47570800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr11:47563000-47570800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr11:47563000-47570800	Weak transcription	Colon Smooth Muscle	Colon
48	chr11:47563000-47571000	Weak transcription	HUVEC	blood vessel
49	chr11:47563000-47572000	Weak transcription	HMEC	breast
50	chr11:47563000-47572000	Weak transcription	HSMM	muscle

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