Variant report

Variant	rs7298818
Chromosome Location	chr12:56396953-56396954
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56396505-56397038	HepG2	liver:	n/a	n/a
2	NR2F2	chr12:56396815-56397020	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56395246..56396955-chr12:56435355..56437007,2	K562	blood:
2	chr12:56388289..56393996-chr12:56394860..56404076,14	K562	blood:
3	chr12:56395394..56397678-chr12:56412069..56414982,2	MCF-7	breast:
4	chr12:56389364..56393818-chr12:56396293..56409099,19	MCF-7	breast:
5	chr12:56395480..56397433-chr12:56414863..56417335,2	MCF-7	breast:
6	chr12:56323919..56326417-chr12:56396111..56398021,2	MCF-7	breast:
7	chr12:56211034..56212554-chr12:56396174..56397733,2	MCF-7	breast:
8	chr12:56372898..56375119-chr12:56396371..56398654,2	MCF-7	breast:

No data

Variant related genes	Relation type
IKZF4	TF binding region
ENSG00000123411	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000237493	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000139531	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11171713	0.81[AMR][1000 genomes]
rs11171714	0.81[AMR][1000 genomes]
rs12099979	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12810011	0.94[EUR][1000 genomes]
rs12815302	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12815387	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12815488	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12817471	0.83[EUR][1000 genomes]
rs12817765	0.81[AMR][1000 genomes]
rs12818756	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12831468	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1614219	0.92[EUR][1000 genomes]
rs1689511	0.89[EUR][1000 genomes]
rs1701706	0.92[EUR][1000 genomes]
rs17118206	0.81[AMR][1000 genomes]
rs17118208	0.81[AMR][1000 genomes]
rs17118262	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2131569	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2456972	0.92[EUR][1000 genomes]
rs2658479	0.89[EUR][1000 genomes]
rs34071823	0.81[AMR][1000 genomes]
rs34228181	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34303864	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34406511	0.94[EUR][1000 genomes]
rs34485293	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34507011	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34602183	0.91[EUR][1000 genomes]
rs34650555	0.94[EUR][1000 genomes]
rs34921584	0.94[EUR][1000 genomes]
rs34962186	0.81[AMR][1000 genomes]
rs35485002	0.91[EUR][1000 genomes]
rs35662491	0.84[EUR][1000 genomes]
rs35666826	0.87[EUR][1000 genomes]
rs35961650	0.89[EUR][1000 genomes]
rs4759022	0.94[EUR][1000 genomes]
rs4759239	0.89[EUR][1000 genomes]
rs71447768	0.81[AMR][1000 genomes]
rs71459326	0.81[AMR][1000 genomes]
rs71459327	0.81[AMR][1000 genomes]
rs71459334	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71459336	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71459339	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71459342	0.87[EUR][1000 genomes]
rs7300772	0.92[EUR][1000 genomes]
rs772919	0.84[EUR][1000 genomes]
rs772922	0.92[EUR][1000 genomes]
rs772923	0.94[EUR][1000 genomes]
rs773115	0.96[EUR][1000 genomes]
rs7963590	0.94[EUR][1000 genomes]
rs7977537	0.89[EUR][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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7298818	SUOX	cis	Thyroid	GTEx
rs7298818	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56391600-56397600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:56391600-56398600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:56391600-56399000	Weak transcription	Primary T cells from cord blood	blood
4	chr12:56391600-56400800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:56391800-56397000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:56391800-56397800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:56391800-56400600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr12:56391800-56400600	Weak transcription	NHEK	skin
9	chr12:56392000-56397400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:56392000-56397400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:56392000-56397600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:56392000-56397600	Weak transcription	HSMM	muscle
13	chr12:56392000-56397800	Weak transcription	HSMMtube	muscle
14	chr12:56392000-56399200	Weak transcription	HUVEC	blood vessel
15	chr12:56392000-56400600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:56392000-56400600	Weak transcription	Fetal Thymus	thymus
17	chr12:56392000-56400600	Weak transcription	Right Atrium	heart
18	chr12:56392000-56400600	Weak transcription	HMEC	breast
19	chr12:56392000-56400800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:56392000-56400800	Weak transcription	GM12878-XiMat	blood
21	chr12:56392200-56399800	Weak transcription	Hela-S3	cervix
22	chr12:56392400-56397400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:56392400-56399400	Strong transcription	Fetal Stomach	stomach
24	chr12:56392400-56400800	Weak transcription	Fetal Brain Male	brain
25	chr12:56392600-56399000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:56393000-56397400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:56393200-56398400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:56393200-56398600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:56394000-56397800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:56394000-56399200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr12:56394200-56397000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:56394400-56399400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr12:56395000-56399200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:56395200-56398600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:56395200-56398800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:56395200-56398800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:56395200-56399400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:56395200-56400000	Strong transcription	Fetal Muscle Leg	muscle
39	chr12:56395400-56398600	Strong transcription	Left Ventricle	heart
40	chr12:56395400-56398800	Strong transcription	Ovary	ovary
41	chr12:56395400-56398800	Strong transcription	Right Ventricle	heart
42	chr12:56395400-56399000	Strong transcription	Brain Angular Gyrus	brain
43	chr12:56395400-56399000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr12:56395400-56399200	Strong transcription	Brain Anterior Caudate	brain
45	chr12:56395600-56398800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:56395600-56398800	Strong transcription	Gastric	stomach
47	chr12:56395600-56399200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr12:56395600-56399200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:56395600-56399200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr12:56395800-56397400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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