Variant report

Variant	rs12469777
Chromosome Location	chr2:183732364-183732365
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	BACH1	chr2:183732098-183732408	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr2:183731826-183732449	H1-neurons	neurons:	n/a	n/a
3	EGR1	chr2:183732254-183732532	K562	blood:	n/a	chr2:183732419-183732432 chr2:183732421-183732431 chr2:183732419-183732432
4	ZBTB7A	chr2:183732106-183732439	HepG2	liver:	n/a	n/a
5	EP300	chr2:183730991-183733542	SK-N-SH	brain:	n/a	chr2:183731819-183731828 chr2:183733039-183733048
6	GATA2	chr2:183730787-183732802	SH-SY5Y	brain:	n/a	chr2:183731573-183731583 chr2:183731575-183731586 chr2:183731575-183731582 chr2:183731575-183731582 chr2:183731575-183731582 chr2:183731572-183731584
7	CTBP2	chr2:183730793-183732591	H1-hESC	embryonic stem cell:	n/a	n/a
8	YY1	chr2:183732252-183732495	SK-N-SH_RA	brain:	n/a	chr2:183732403-183732413 chr2:183732402-183732418
9	POLR2A	chr2:183731651-183732476	H1-neurons	neurons:	n/a	n/a
10	SIN3A	chr2:183730776-183732404	H1-hESC	embryonic stem cell:	n/a	n/a
11	YY1	chr2:183732175-183732505	H1-hESC	embryonic stem cell:	n/a	chr2:183732403-183732413 chr2:183732402-183732418
12	ZNF384	chr2:183732318-183732631	K562	blood:	n/a	chr2:183732533-183732541

Variant related genes	Relation type
FRZB	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10182016	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10202627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10803961	0.90[ASN][1000 genomes]
rs10931044	0.88[ASN][1000 genomes]
rs10931045	0.90[ASN][1000 genomes]
rs10931046	0.90[ASN][1000 genomes]
rs10931049	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11686953	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11900716	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12466685	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12471947	0.84[AMR][1000 genomes]
rs12473127	0.90[ASN][1000 genomes]
rs12476544	0.86[ASN][1000 genomes]
rs12476897	0.90[ASN][1000 genomes]
rs12611837	0.82[ASN][1000 genomes]
rs12693326	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12693327	0.86[ASN][1000 genomes]
rs12990735	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12992123	0.90[ASN][1000 genomes]
rs13026760	0.90[ASN][1000 genomes]
rs1584734	0.90[ASN][1000 genomes]
rs2100344	0.90[ASN][1000 genomes]
rs2118590	0.90[ASN][1000 genomes]
rs21714	0.88[ASN][1000 genomes]
rs288247	0.88[ASN][1000 genomes]
rs288248	0.88[ASN][1000 genomes]
rs288249	0.87[ASN][1000 genomes]
rs288330	0.84[ASN][1000 genomes]
rs2887227	0.90[ASN][1000 genomes]
rs34528848	0.90[ASN][1000 genomes]
rs409238	0.89[ASN][1000 genomes]
rs4293535	0.97[ASN][1000 genomes]
rs430350	0.90[ASN][1000 genomes]
rs4311031	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4338928	0.90[ASN][1000 genomes]
rs4581857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4666867	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55899538	0.90[ASN][1000 genomes]
rs59146529	0.90[ASN][1000 genomes]
rs6433991	0.90[ASN][1000 genomes]
rs6433992	0.89[ASN][1000 genomes]
rs6433994	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs722738	0.88[ASN][1000 genomes]
rs74178517	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7560782	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7562344	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7564919	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7605198	0.86[ASN][1000 genomes]
rs825529	0.82[ASN][1000 genomes]
rs9973404	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2757842	chr2:183437700-183835084	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759104	chr2:183437700-183835084	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2756954	chr2:183528670-183764930	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv34847	chr2:183537399-183786763	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1006265	chr2:183666013-183777604	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv536071	chr2:183666013-183777604	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv818096	chr2:183701588-183827018	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv875484	chr2:183702964-183747442	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12469777	FRZB	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183728200-183732400	Active TSS	Aorta	Aorta
2	chr2:183729200-183732400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:183729600-183732400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:183729800-183732400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr2:183729800-183732400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr2:183730000-183732600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:183730000-183732800	Active TSS	Brain Angular Gyrus	brain
8	chr2:183730400-183732400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr2:183730400-183732400	Active TSS	Brain Hippocampus Middle	brain
10	chr2:183730600-183732400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr2:183730600-183732400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:183730600-183732400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:183730600-183732400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:183730800-183732400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr2:183730800-183732400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
16	chr2:183730800-183732400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:183730800-183732400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
18	chr2:183730800-183732400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:183730800-183732400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:183730800-183732400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr2:183730800-183732400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:183730800-183732400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:183730800-183732400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:183730800-183732400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
25	chr2:183730800-183732400	Flanking Bivalent TSS/Enh	HepG2	liver
26	chr2:183730800-183732600	Active TSS	Brain Substantia Nigra	brain
27	chr2:183730800-183732600	Active TSS	Rectal Smooth Muscle	rectum
28	chr2:183731000-183732400	Bivalent/Poised TSS	Primary B cells from cord blood	blood
29	chr2:183731000-183732400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:183731200-183732400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr2:183731200-183732400	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr2:183731200-183732400	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr2:183731200-183732400	Active TSS	Right Atrium	heart
34	chr2:183731200-183732400	Active TSS	HSMM	muscle
35	chr2:183731200-183732600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
36	chr2:183731200-183732600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
37	chr2:183731400-183732400	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr2:183731400-183732400	Flanking Active TSS	HUVEC	blood vessel
39	chr2:183731600-183732400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr2:183731600-183732400	Bivalent Enhancer	Stomach Mucosa	stomach
41	chr2:183731600-183733000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
42	chr2:183731800-183732400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:183731800-183732400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
44	chr2:183731800-183732400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
45	chr2:183731800-183732400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
46	chr2:183731800-183732400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:183731800-183732400	Flanking Active TSS	Colonic Mucosa	Colon
48	chr2:183731800-183732400	Flanking Active TSS	Fetal Intestine Small	intestine
49	chr2:183731800-183732600	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr2:183731800-183733000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood

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