Variant report

Variant	rs12798346
Chromosome Location	chr11:47583121-47583122
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	CTCF	chr11:47583080-47583230	Caco-2	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:47582289..47584764-chr11:47585260..47588295,3	K562	blood:
2	chr11:47574386..47578054-chr11:47581653..47584758,3	K562	blood:
3	chr11:47581879..47583794-chr11:47585502..47588338,2	MCF-7	breast:
4	chr11:47576405..47578054-chr11:47582418..47584611,2	K562	blood:

Variant related genes	Relation type
PTPMT1	TF binding region
NDUFS3	TF binding region
RN7SL652P	TF binding region
ENSG00000213619	Chromatin interaction
ENSG00000149187	Chromatin interaction
ENSG00000110536	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1064608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10742803	0.87[CEU][hapmap]
rs10769258	0.89[CEU][hapmap];0.90[CHB][hapmap];0.83[GIH][hapmap]
rs10769262	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs10838698	0.89[CEU][hapmap];0.90[CHB][hapmap];0.83[GIH][hapmap]
rs10838699	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs10838708	0.90[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs10838724	0.83[ASN][1000 genomes]
rs10838738	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10838747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs10838748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs10838757	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs11039212	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs11039255	0.80[ASN][1000 genomes]
rs11039307	0.94[ASN][1000 genomes]
rs11039308	0.87[ASN][1000 genomes]
rs11039342	0.82[AMR][1000 genomes]
rs11601603	0.89[CEU][hapmap]
rs11604680	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11605348	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11605672	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs12363232	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12419692	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12787112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs12794570	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12798028	0.97[ASN][1000 genomes]
rs12799623	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1317149	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs17788930	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs2030166	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053979	0.86[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs2293577	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs2293578	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs2868459	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs34958982	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs35184771	0.80[ASN][1000 genomes]
rs3781625	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs3781626	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs3781627	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs3817334	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs3817335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4752845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs4752856	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4752857	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]
rs4752990	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs4752993	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap]
rs4752994	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs4752999	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs4992357	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap]
rs56400411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6485753	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs66749409	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7124681	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs755553	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs755554	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7927771	1.00[CEU][hapmap]
rs7928842	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7937331	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs7940536	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs7945473	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs896816	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap]

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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12798346	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs12798346	C1QTNF4	cis	lung	GTEx
rs12798346	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs12798346	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs12798346	C1QTNF4	cis	Muscle Skeletal	GTEx
rs12798346	SPI1	cis	lymphoblastoid	seeQTL
rs12798346	ACP2	cis	lymphoblastoid	seeQTL
rs12798346	C1QTNF4	cis	lymphoblastoid	seeQTL
rs12798346	SLC35C1	cis	parietal	SCAN
rs12798346	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs12798346	MADD	cis	cerebellum	SCAN
rs12798346	MTCH2	cis	cerebellum	SCAN
rs12798346	C1QTNF4	cis	Artery Tibial	GTEx
rs12798346	C1QTNF4	cis	Whole Blood	GTEx
rs12798346	C1QTNF4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47575200-47586000	Weak transcription	HSMMtube	muscle
2	chr11:47575200-47586200	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr11:47575200-47586200	Weak transcription	Placenta	Placenta
4	chr11:47575200-47586400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:47575200-47586400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr11:47575200-47586400	Weak transcription	Psoas Muscle	Psoas
7	chr11:47575200-47586600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr11:47575200-47586600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:47575200-47586600	Weak transcription	Gastric	stomach
10	chr11:47575200-47586600	Weak transcription	Ovary	ovary
11	chr11:47575400-47586000	Weak transcription	Primary B cells from cord blood	blood
12	chr11:47575400-47586200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:47575400-47586200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:47575400-47586200	Weak transcription	Fetal Muscle Leg	muscle
15	chr11:47575400-47586200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr11:47575400-47586200	Weak transcription	A549	lung
17	chr11:47575400-47586200	Weak transcription	NHEK	skin
18	chr11:47575400-47586400	Weak transcription	Brain Angular Gyrus	brain
19	chr11:47575400-47586400	Weak transcription	Fetal Stomach	stomach
20	chr11:47575400-47586400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr11:47575400-47586400	Weak transcription	NH-A	brain
22	chr11:47575600-47584400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr11:47575600-47585800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:47575600-47585800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr11:47575600-47586200	Weak transcription	NHDF-Ad	bronchial
26	chr11:47575600-47586600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr11:47575800-47586200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr11:47576000-47586000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr11:47576200-47585800	Weak transcription	Dnd41	blood
30	chr11:47576200-47586200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:47578400-47586600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:47582200-47585800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr11:47582200-47585800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:47582200-47586000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:47582400-47584400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:47582400-47585800	Weak transcription	Hela-S3	cervix
37	chr11:47582400-47586000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr11:47582400-47586200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:47582400-47586200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr11:47582400-47586200	Weak transcription	Fetal Brain Female	brain
41	chr11:47582400-47586400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr11:47582400-47586400	Weak transcription	Adipose Nuclei	Adipose
43	chr11:47582400-47586400	Weak transcription	Osteobl	bone
44	chr11:47582600-47585400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr11:47582600-47586400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:47582600-47586400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr11:47582800-47586200	Weak transcription	Primary monocytes fromperipheralblood	blood

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