Variant report

Variant	rs4752857
Chromosome Location	chr11:47655752-47655753
allele	C/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	POLR2A	chr11:47655520-47655814	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:47650534..47652404-chr11:47653064..47655999,2	MCF-7	breast:
2	chr11:47655561..47657543-chr11:47662606..47665556,2	K562	blood:
3	chr11:47654513..47656961-chr11:47662854..47665133,2	MCF-7	breast:
4	chr11:47655594..47657226-chr11:47658278..47659810,2	K562	blood:

Variant related genes	Relation type
MTCH2	TF binding region
ENSG00000109919	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1064608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10838738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10838747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10838748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10838757	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11039307	0.83[ASN][1000 genomes]
rs11039308	0.97[ASN][1000 genomes]
rs11039324	0.91[ASN][1000 genomes]
rs11039342	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11039348	0.83[ASN][1000 genomes]
rs11039355	0.81[ASN][1000 genomes]
rs11602339	0.80[ASN][1000 genomes]
rs11602395	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11604680	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11604825	0.82[ASN][1000 genomes]
rs11605348	0.81[AMR][1000 genomes]
rs12361031	0.80[ASN][1000 genomes]
rs12363232	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12419507	0.92[ASN][1000 genomes]
rs12419692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12421210	0.82[ASN][1000 genomes]
rs12787112	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12787646	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12794570	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12798028	0.84[ASN][1000 genomes]
rs12798346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12799623	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12803191	0.82[ASN][1000 genomes]
rs1317149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs17788930	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs2030166	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2290850	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs34910028	0.83[ASN][1000 genomes]
rs34923397	0.81[ASN][1000 genomes]
rs34958982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3817334	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3817335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4752856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56400411	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59360790	0.95[ASN][1000 genomes]
rs66749409	0.85[ASN][1000 genomes]
rs7105282	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7124681	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7927771	1.00[CEU][hapmap];0.80[ASN][1000 genomes]
rs7928842	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7947730	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs9909	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4752857	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs4752857	C1QTNF4	cis	Whole Blood	GTEx
rs4752857	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs4752857	C1QTNF4	cis	Artery Tibial	GTEx
rs4752857	C1QTNF4	cis	lung	GTEx
rs4752857	C1QTNF4	cis	Muscle Skeletal	GTEx
rs4752857	SPI1	cis	multi-tissue	Pritchard
rs4752857	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs4752857	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs4752857	C1QTNF4	cis	multi-tissue	Pritchard
rs4752857	Hs.6637	cis	multi-tissue	Pritchard
rs4752857	C1QTNF4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47636600-47661400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:47637600-47657200	Strong transcription	Primary B cells from peripheral blood	blood
3	chr11:47637600-47660800	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr11:47637600-47661200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:47637600-47663200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:47637800-47660400	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr11:47637800-47661000	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr11:47637800-47661000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr11:47638000-47661400	Strong transcription	Fetal Thymus	thymus
10	chr11:47638000-47661800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:47638200-47661200	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr11:47638200-47661200	Strong transcription	Stomach Smooth Muscle	stomach
13	chr11:47638200-47661600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:47638200-47661600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:47638400-47660400	Strong transcription	Dnd41	blood
16	chr11:47638400-47661200	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr11:47638600-47657200	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr11:47638800-47661600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr11:47639000-47658000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr11:47639000-47661200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:47639000-47661400	Strong transcription	Fetal Muscle Leg	muscle
22	chr11:47639000-47662600	Weak transcription	Stomach Mucosa	stomach
23	chr11:47639200-47657600	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr11:47639600-47661200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr11:47639800-47657600	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:47640000-47661000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:47640200-47661200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr11:47640200-47661200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr11:47640200-47661200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:47640600-47661400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:47640800-47661400	Strong transcription	Fetal Intestine Small	intestine
32	chr11:47640800-47661400	Strong transcription	Fetal Stomach	stomach
33	chr11:47641800-47657600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr11:47641800-47657600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr11:47641800-47659200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr11:47641800-47661200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr11:47641800-47661600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:47642000-47661400	Strong transcription	Placenta	Placenta
39	chr11:47642000-47661800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:47643400-47661200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr11:47644000-47661600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:47645000-47657200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr11:47646800-47657800	Strong transcription	HUVEC	blood vessel
44	chr11:47646800-47662600	Weak transcription	Aorta	Aorta
45	chr11:47647200-47657200	Strong transcription	NHEK	skin
46	chr11:47648200-47662800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr11:47648200-47663200	Weak transcription	Gastric	stomach
48	chr11:47648400-47656600	Weak transcription	Right Ventricle	heart
49	chr11:47648400-47662800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr11:47649200-47662600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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