Variant report

Variant	rs4752797
Chromosome Location	chr11:47874364-47874365
allele	A/G
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	ZKSCAN1	chr11:47874310-47874386	Hela-S3	cervix:	n/a	n/a
2	FOS	chr11:47874353-47874510	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:47868432..47872224-chr11:47874279..47876068,4	MCF-7	breast:
2	chr11:47869337..47872493-chr11:47872959..47875710,4	MCF-7	breast:
3	chr11:47873347..47874902-chr11:47878009..47880856,2	MCF-7	breast:
4	chr11:47631158..47632846-chr11:47873541..47876421,2	MCF-7	breast:

Variant related genes	Relation type
NUP160	TF binding region
ENSG00000030066	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10838747	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs10838748	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs10838757	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039355	0.81[AMR][1000 genomes]
rs11039389	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039390	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039391	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039416	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039426	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039433	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11602339	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11605774	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12361031	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12361256	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12364432	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12418852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12421210	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12785833	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12787112	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12787330	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12798109	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12803191	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17788930	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2290850	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34128973	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34614231	0.86[AMR][1000 genomes]
rs34910028	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34923397	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35805829	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35902101	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35985502	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752801	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4752873	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7105282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7120333	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7130758	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7927771	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7947730	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	nsv1049835	chr11:47837089-47928822	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv541036	chr11:47837089-47928822	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs4752797	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs4752797	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs4752797	MADD	cis	cerebellum	SCAN
rs4752797	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs4752797	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs4752797	SLC35C1	cis	parietal	SCAN
rs4752797	SPI1	cis	lymphoblastoid	seeQTL
rs4752797	C1QTNF4	cis	Muscle Skeletal	GTEx
rs4752797	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs4752797	C1QTNF4	cis	lung	GTEx
rs4752797	SPI1	cis	multi-tissue	Pritchard
rs4752797	C1QTNF4	cis	Whole Blood	GTEx
rs4752797	MTCH2	cis	cerebellum	SCAN
rs4752797	NR1H3	cis	multi-tissue	Pritchard
rs4752797	C1QTNF4	cis	lymphoblastoid	seeQTL
rs4752797	MYBPC3	cis	multi-tissue	Pritchard

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47870600-47875200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:47870600-47877400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:47870600-47879600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr11:47870600-47885400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:47870800-47875200	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr11:47870800-47877600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr11:47870800-47877800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr11:47870800-47877800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr11:47870800-47879200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr11:47870800-47879800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:47870800-47889400	Enhancers	Primary B cells from peripheral blood	blood
12	chr11:47871000-47875200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr11:47871000-47875200	Weak transcription	Fetal Kidney	kidney
14	chr11:47871000-47875200	Weak transcription	Placenta	Placenta
15	chr11:47871000-47875200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr11:47871000-47877600	Weak transcription	K562	blood
17	chr11:47871000-47883200	Weak transcription	NHDF-Ad	bronchial
18	chr11:47871200-47877800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:47872200-47875200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:47872200-47877600	Enhancers	Primary B cells from cord blood	blood
21	chr11:47872200-47884000	Weak transcription	Thymus	Thymus
22	chr11:47872400-47874800	Enhancers	GM12878-XiMat	blood
23	chr11:47872400-47879400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr11:47872800-47874800	Weak transcription	Dnd41	blood
25	chr11:47872800-47875200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:47872800-47879000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:47872800-47881200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:47873000-47883400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr11:47873000-47884600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr11:47873200-47875200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr11:47873200-47875200	Weak transcription	Fetal Thymus	thymus
32	chr11:47873200-47876000	Enhancers	A549	lung
33	chr11:47873200-47877600	Enhancers	Hela-S3	cervix
34	chr11:47873200-47879600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr11:47873200-47880600	Weak transcription	Primary T cells from cord blood	blood
36	chr11:47873400-47874800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr11:47873400-47875000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr11:47873400-47883200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr11:47873600-47874800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr11:47873600-47875000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr11:47873600-47879200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr11:47873800-47874800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:47874200-47875200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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