Variant report

Variant	rs12421210
Chromosome Location	chr11:47779586-47779587
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:47778981-47779989	GM12891	blood:	n/a	n/a
2	POLR2A	chr11:47779050-47780327	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:47779025-47780262	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr11:47779523-47780122	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr11:47779184-47780001	K562	blood:	n/a	n/a
6	POLR2A	chr11:47778950-47780786	GM12891	blood:	n/a	n/a
7	POLR2A	chr11:47779411-47779696	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr11:47779187-47779621	K562	blood:	n/a	n/a
9	POLR2A	chr11:47779537-47780227	A549	lung:	n/a	n/a
10	POLR2A	chr11:47778963-47780334	GM12891	blood:	n/a	n/a
11	POLR2A	chr11:47779099-47780345	GM12892	blood:	n/a	n/a
12	POLR2A	chr11:47779013-47780978	GM12891	blood:	n/a	n/a
13	POLR2A	chr11:47779322-47780125	K562	blood:	n/a	n/a
14	POLR2A	chr11:47779182-47780274	HepG2	liver:	n/a	n/a
15	POLR2A	chr11:47778695-47781147	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:47779558-47780084	HL-60	blood:	n/a	n/a
17	POLR2A	chr11:47779539-47780106	K562	blood:	n/a	n/a
18	POLR2A	chr11:47778930-47780864	GM12892	blood:	n/a	n/a
19	POLR2A	chr11:47778619-47780198	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr11:47779313-47779801	HepG2	liver:	n/a	n/a
21	POLR2A	chr11:47779236-47780270	K562	blood:	n/a	n/a
22	POLR2A	chr11:47779164-47780071	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr11:47778907-47781201	GM12892	blood:	n/a	n/a
24	POLR2A	chr11:47778606-47781074	GM12892	blood:	n/a	n/a
25	POLR2A	chr11:47778984-47780129	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr11:47778725-47780836	HepG2	liver:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47772923..47774749-chr11:47778974..47781299,2	MCF-7	breast:
2	chr11:47777903..47779990-chr11:47786996..47788801,2	K562	blood:

No data

Variant related genes	Relation type
FNBP4	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1064608	0.81[ASN][1000 genomes]
rs10838738	0.81[ASN][1000 genomes]
rs10838747	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838748	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838757	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039308	0.82[ASN][1000 genomes]
rs11039324	0.82[ASN][1000 genomes]
rs11039342	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039348	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11039355	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039389	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039390	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039391	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039416	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039426	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039433	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11602339	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11602395	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11604825	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11605774	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12361031	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12364432	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12418852	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12419692	0.82[ASN][1000 genomes]
rs12785833	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12787112	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12787330	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12787646	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12794570	0.82[ASN][1000 genomes]
rs12798109	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12803191	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17788930	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290850	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34128973	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34910028	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34923397	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35805829	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35902101	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35985502	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3817334	0.82[ASN][1000 genomes]
rs3817335	0.82[ASN][1000 genomes]
rs4752797	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4752856	0.82[ASN][1000 genomes]
rs4752857	0.82[ASN][1000 genomes]
rs4752873	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59360790	0.83[ASN][1000 genomes]
rs7105282	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7120333	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7130758	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7927771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7947730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9909	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[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	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
2	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
3	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
4	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12421210	C1QTNF4	cis	Muscle Skeletal	GTEx
rs12421210	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs12421210	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs12421210	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs12421210	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs12421210	C1QTNF4	cis	lung	GTEx
rs12421210	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs12421210	C1QTNF4	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47737000-47786200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:47737200-47779800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:47737800-47782800	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr11:47737800-47785800	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr11:47737800-47786000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr11:47737800-47786200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:47737800-47786200	Strong transcription	Muscle Satellite Cultured Cells	--
8	chr11:47737800-47786400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:47737800-47786400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr11:47737800-47786400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:47737800-47786400	Strong transcription	Fetal Thymus	thymus
12	chr11:47737800-47786800	Strong transcription	Placenta	Placenta
13	chr11:47738000-47786200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:47738000-47786400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:47738000-47786400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr11:47738000-47786800	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:47738200-47786400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:47738400-47786200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:47738600-47785800	Strong transcription	Dnd41	blood
20	chr11:47746200-47786000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:47746400-47786200	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr11:47747400-47786200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr11:47747600-47786400	Strong transcription	Fetal Intestine Large	intestine
24	chr11:47747800-47786200	Strong transcription	A549	lung
25	chr11:47748000-47786000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr11:47748600-47786200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:47748600-47786200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr11:47748800-47786200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr11:47753400-47786400	Strong transcription	Liver	Liver
30	chr11:47753600-47786400	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr11:47759200-47786200	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr11:47759400-47785400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr11:47760600-47783200	Strong transcription	Fetal Lung	lung
34	chr11:47764800-47780200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:47764800-47786200	Strong transcription	HSMM	muscle
36	chr11:47765200-47780400	Strong transcription	NHDF-Ad	bronchial
37	chr11:47766600-47779600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr11:47768000-47786600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr11:47769000-47779600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:47769000-47787600	Weak transcription	Stomach Mucosa	stomach
41	chr11:47769600-47786000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr11:47769800-47779600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr11:47773600-47779600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:47776000-47787400	Weak transcription	Psoas Muscle	Psoas
45	chr11:47776200-47779600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr11:47776200-47779600	Weak transcription	Fetal Brain Male	brain
47	chr11:47776200-47779800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr11:47776400-47779600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr11:47776400-47779600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr11:47776400-47779600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links