Variant report

Variant	rs12798109
Chromosome Location	chr11:47889850-47889851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47880257..47883214-chr11:47889467..47892420,2	K562	blood:
2	chr11:47875918..47878911-chr11:47889352..47891666,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10838757	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039355	0.81[AMR][1000 genomes]
rs11039389	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039390	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039391	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039416	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039426	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039433	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11602339	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11602395	0.81[EUR][1000 genomes]
rs11605774	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12361031	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12361256	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12364432	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12418852	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12421210	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12785833	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12787330	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12803191	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17788930	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2290850	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34128973	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34614231	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34910028	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34923397	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35805829	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35902101	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35985502	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752797	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752801	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4752873	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7105282	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7120333	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7130758	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7927771	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7947730	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9909	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[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	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	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
3	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
4	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
5	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12798109	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs12798109	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs12798109	C1QTNF4	cis	lung	GTEx
rs12798109	C1QTNF4	cis	Whole Blood	GTEx
rs12798109	C1QTNF4	cis	Muscle Skeletal	GTEx
rs12798109	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs12798109	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs12798109	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47880000-47891000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr11:47880200-47891000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:47886000-47891200	Weak transcription	Spleen	Spleen
4	chr11:47886000-47891600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr11:47886200-47891000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr11:47886200-47891200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:47886800-47890800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:47886800-47891000	Weak transcription	NH-A	brain
9	chr11:47887000-47891000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:47887000-47891000	Weak transcription	HUVEC	blood vessel
11	chr11:47887000-47891000	Weak transcription	Osteobl	bone
12	chr11:47887000-47891200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:47887000-47891200	Weak transcription	HSMMtube	muscle
14	chr11:47887000-47891200	Weak transcription	NHLF	lung
15	chr11:47887000-47891400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:47887000-47892000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:47887200-47891000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr11:47887200-47891000	Weak transcription	HSMM	muscle
19	chr11:47888600-47891000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr11:47889200-47890000	Enhancers	NHDF-Ad	bronchial
21	chr11:47889200-47891000	Enhancers	Hela-S3	cervix
22	chr11:47889200-47891200	Weak transcription	Primary B cells from cord blood	blood
23	chr11:47889400-47891000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr11:47889400-47891200	Enhancers	A549	lung
25	chr11:47889800-47891200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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