Variant report

Variant	rs56400411
Chromosome Location	chr11:47586376-47586377
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr11:47586281-47586613	T-47D	breast:	n/a	chr11:47586460-47586472 chr11:47586486-47586501
2	MXI1	chr11:47586366-47587741	IMR90	lung:	n/a	n/a
3	MXI1	chr11:47586309-47588022	SK-N-SH	brain:	n/a	n/a
4	E2F6	chr11:47586362-47587689	H1-hESC	embryonic stem cell:	n/a	chr11:47586954-47586961 chr11:47586698-47586706 chr11:47586953-47586965 chr11:47586953-47586962 chr11:47586954-47586961 chr11:47586954-47586961 chr11:47586697-47586707 chr11:47586952-47586963 chr11:47586949-47586964 chr11:47587573-47587582 chr11:47586698-47586705 chr11:47586698-47586706
5	MTA3	chr11:47586352-47587692	GM12878	blood:	n/a	n/a
6	FOXA1	chr11:47586247-47586744	HepG2	liver:	n/a	chr11:47586460-47586472 chr11:47586486-47586501
7	FOXA2	chr11:47586281-47586810	A549	lung:	n/a	chr11:47586460-47586472
8	FOXA1	chr11:47586295-47586705	HepG2	liver:	n/a	chr11:47586460-47586472 chr11:47586486-47586501
9	FOXA2	chr11:47586334-47586622	HepG2	liver:	n/a	chr11:47586460-47586472
10	FOXA2	chr11:47586273-47586807	A549	lung:	n/a	chr11:47586460-47586472
11	FOXA1	chr11:47586248-47586781	HepG2	liver:	n/a	chr11:47586460-47586472 chr11:47586486-47586501
12	FOXA1	chr11:47586241-47586763	HepG2	liver:	n/a	chr11:47586460-47586472 chr11:47586486-47586501

No.	Distal block	Cell Line	Cell type
1	chr11:47535507..47539459-chr11:47585714..47589149,4	MCF-7	breast:
2	chr11:47535966..47537826-chr11:47584643..47586708,2	K562	blood:
3	chr11:47585806..47587545-chr6:74230961..74233222,2	K562	blood:
4	chr11:47571371..47576564-chr11:47585605..47588889,10	MCF-7	breast:
5	chr11:47586161..47588765-chr11:47660200..47662976,2	MCF-7	breast:
6	chr11:47515223..47517618-chr11:47586025..47588780,2	K562	blood:
7	chr11:47585423..47588969-chr11:47597747..47604797,13	K562	blood:
8	chr11:47571923..47578059-chr11:47583779..47591283,17	MCF-7	breast:
9	chr11:47578751..47581226-chr11:47586015..47587663,2	K562	blood:
10	chr11:47429691..47431699-chr11:47584830..47587245,2	MCF-7	breast:

Variant related genes	Relation type
PTPMT1	TF binding region
NDUFS3	TF binding region
ENSG00000165915	Chromatin interaction
ENSG00000255197	Chromatin interaction
ENSG00000270072	Chromatin interaction
ENSG00000200376	Chromatin interaction
ENSG00000149187	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000213619	Chromatin interaction
ENSG00000123444	Chromatin interaction
ENSG00000231880	Chromatin interaction
ENSG00000265559	Chromatin interaction
ENSG00000109919	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1064608	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10838724	0.83[ASN][1000 genomes]
rs10838738	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10838747	0.82[AMR][1000 genomes]
rs11039307	0.93[ASN][1000 genomes]
rs11039308	0.86[ASN][1000 genomes]
rs11039342	0.82[AMR][1000 genomes]
rs11605348	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12363232	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12419692	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12787112	0.81[AMR][1000 genomes]
rs12794570	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12798028	0.96[ASN][1000 genomes]
rs12798346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12799623	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1317149	0.82[ASN][1000 genomes]
rs2030166	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34958982	0.83[ASN][1000 genomes]
rs3817334	0.83[ASN][1000 genomes]
rs3817335	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4752845	0.84[ASN][1000 genomes]
rs4752856	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4752857	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66749409	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7124681	0.82[ASN][1000 genomes]
rs7928842	0.86[ASN][1000 genomes]
rs7945473	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs56400411	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs56400411	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs56400411	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs56400411	C1QTNF4	cis	lung	GTEx
rs56400411	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs56400411	C1QTNF4	cis	Whole Blood	GTEx
rs56400411	C1QTNF4	cis	Artery Tibial	GTEx
rs56400411	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs56400411	C1QTNF4	cis	Muscle Skeletal	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47575200-47586400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:47575200-47586400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr11:47575200-47586400	Weak transcription	Psoas Muscle	Psoas
4	chr11:47575200-47586600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:47575200-47586600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:47575200-47586600	Weak transcription	Gastric	stomach
7	chr11:47575200-47586600	Weak transcription	Ovary	ovary
8	chr11:47575400-47586400	Weak transcription	Brain Angular Gyrus	brain
9	chr11:47575400-47586400	Weak transcription	Fetal Stomach	stomach
10	chr11:47575400-47586400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr11:47575400-47586400	Weak transcription	NH-A	brain
12	chr11:47575600-47586600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:47578400-47586600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:47582400-47586400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:47582400-47586400	Weak transcription	Adipose Nuclei	Adipose
16	chr11:47582400-47586400	Weak transcription	Osteobl	bone
17	chr11:47582600-47586400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:47582600-47586400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr11:47584800-47586400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr11:47585800-47586400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr11:47585800-47586400	Enhancers	Primary T cells from cord blood	blood
22	chr11:47585800-47586400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr11:47585800-47586400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr11:47585800-47586400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr11:47585800-47586400	Enhancers	Pancreas	Pancrea
26	chr11:47585800-47586600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr11:47585800-47586600	Enhancers	Primary B cells from peripheral blood	blood
28	chr11:47585800-47586600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr11:47586000-47586400	Enhancers	Primary B cells from cord blood	blood
30	chr11:47586000-47586400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr11:47586000-47586400	Enhancers	Liver	Liver
32	chr11:47586000-47586400	Enhancers	HSMMtube	muscle
33	chr11:47586000-47586400	Enhancers	K562	blood
34	chr11:47586000-47586600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr11:47586000-47587000	Flanking Active TSS	Hela-S3	cervix
36	chr11:47586200-47586400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr11:47586200-47586400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr11:47586200-47586400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr11:47586200-47586400	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr11:47586200-47586400	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr11:47586200-47586400	Enhancers	Primary hematopoietic stem cells	blood
42	chr11:47586200-47586400	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr11:47586200-47586400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr11:47586200-47586400	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr11:47586200-47586400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:47586200-47586400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:47586200-47586400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr11:47586200-47586400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr11:47586200-47586400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:47586200-47586400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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