Variant report

Variant	rs13408372
Chromosome Location	chr2:98962749-98962750
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	REST	chr2:98962673-98963718	H1-hESC	embryonic stem cell:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
2	REST	chr2:98962703-98963530	H1-hESC	embryonic stem cell:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
3	REST	chr2:98962720-98963714	SK-N-SH	brain:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
4	REST	chr2:98962715-98963559	PANC-1	pancreas:	n/a	chr2:98963441-98963454 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98963150-98963164 chr2:98962956-98962969 chr2:98963152-98963162 chr2:98963144-98963164
5	REST	chr2:98962659-98963649	PFSK-1	brain:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
6	REST	chr2:98962583-98963636	U87	brain:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
7	MAZ	chr2:98962678-98963362	IMR90	lung:	n/a	n/a
8	REST	chr2:98962726-98963491	K562	blood:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
9	REST	chr2:98962468-98963925	PFSK-1	brain:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
10	REST	chr2:98962630-98963664	HL-60	blood:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
11	BACH1	chr2:98962723-98963173	H1-hESC	embryonic stem cell:	n/a	n/a
12	REST	chr2:98962711-98963476	PFSK-1	brain:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
13	REST	chr2:98962708-98963486	U87	brain:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
14	ZNF263	chr2:98962551-98963538	HEK293-T-REx	kidney:	n/a	chr2:98962940-98962949
15	REST	chr2:98962617-98963720	HL-60	blood:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
16	REST	chr2:98962602-98963697	ECC-1	luminal epithelium:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
17	SUZ12	chr2:98962542-98964708	NT2-D1	testis:	n/a	n/a
18	CTBP2	chr2:98962728-98964927	H1-hESC	embryonic stem cell:	n/a	n/a
19	REST	chr2:98962583-98963634	U87	brain:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
20	REST	chr2:98962585-98963536	PANC-1	pancreas:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
21	REST	chr2:98962648-98963603	H1-neurons	neurons:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
22	REST	chr2:98962699-98963492	A549	lung:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
23	REST	chr2:98962648-98963427	PANC-1	pancreas:	n/a	chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164
24	REST	chr2:98962537-98964437	ECC-1	luminal epithelium:	n/a	chr2:98963441-98963454 chr2:98963144-98963164 chr2:98963152-98963162 chr2:98963137-98963146 chr2:98962936-98962949 chr2:98963144-98963164 chr2:98963145-98963163 chr2:98962956-98962969 chr2:98963150-98963164

Variant related genes	Relation type
ENSG00000227987	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10172229	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10172281	0.96[ASN][1000 genomes]
rs10181000	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10190679	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10199476	0.85[CHB][hapmap]
rs10210685	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11124096	0.85[CHB][hapmap]
rs11889349	0.85[CHB][hapmap]
rs11895654	0.85[CHB][hapmap]
rs13394706	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13427344	1.00[ASN][1000 genomes]
rs13428221	0.91[ASN][1000 genomes]
rs13432099	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1451251	0.85[CHB][hapmap]
rs1466944	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs17429208	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2055591	0.98[ASN][1000 genomes]
rs2102270	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2122756	0.85[CHB][hapmap]
rs2221416	0.85[CHB][hapmap]
rs2292118	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4374424	0.85[CHB][hapmap]
rs4455212	0.85[CHB][hapmap]
rs4477970	0.85[CHB][hapmap]
rs4632400	0.85[CHB][hapmap]
rs4851951	0.83[CHB][hapmap]
rs4851953	0.93[EUR][1000 genomes]
rs56320609	0.96[ASN][1000 genomes]
rs60924437	0.99[ASN][1000 genomes]
rs62156263	0.99[ASN][1000 genomes]
rs62156264	0.99[ASN][1000 genomes]
rs6542732	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6543419	0.85[CHB][hapmap]
rs6715989	0.85[CHB][hapmap]
rs6725543	0.85[CHB][hapmap]
rs6747410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs6753286	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6754222	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs72819909	0.98[ASN][1000 genomes]
rs72950941	0.80[AMR][1000 genomes]
rs7571001	1.00[ASN][1000 genomes]
rs7571110	1.00[ASN][1000 genomes]
rs7580008	1.00[ASN][1000 genomes]
rs7586663	1.00[ASN][1000 genomes]
rs7606220	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1008645	chr2:98915767-99010743	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1010466	chr2:98938886-98998109	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1013617	chr2:98943377-99004173	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13408372	CNGA3	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98962000-98964400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr2:98962400-98964200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr2:98962400-98964800	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr2:98962600-98962800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
5	chr2:98962600-98962800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
6	chr2:98962600-98962800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:98962600-98962800	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:98962600-98962800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
9	chr2:98962600-98962800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:98962600-98962800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:98962600-98962800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:98962600-98962800	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:98962600-98962800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:98962600-98962800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:98962600-98962800	Bivalent Enhancer	Brain Germinal Matrix	brain
16	chr2:98962600-98962800	Bivalent Enhancer	Brain Hippocampus Middle	brain
17	chr2:98962600-98962800	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
18	chr2:98962600-98962800	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
19	chr2:98962600-98962800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
20	chr2:98962600-98962800	Flanking Bivalent TSS/Enh	HSMM	muscle
21	chr2:98962600-98962800	Flanking Bivalent TSS/Enh	NHDF-Ad	bronchial
22	chr2:98962600-98962800	Bivalent Enhancer	NHEK	skin
23	chr2:98962600-98962800	Flanking Bivalent TSS/Enh	Osteobl	bone
24	chr2:98962600-98963000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:98962600-98963000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:98962600-98963000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:98962600-98963000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:98962600-98963000	Enhancers	Pancreas	Pancrea
29	chr2:98962600-98963000	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
30	chr2:98962600-98963200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:98962600-98963200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
32	chr2:98962600-98963200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
33	chr2:98962600-98963200	Enhancers	Gastric	stomach
34	chr2:98962600-98963200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
35	chr2:98962600-98963400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:98962600-98963400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
37	chr2:98962600-98963400	Bivalent/Poised TSS	NHLF	lung
38	chr2:98962600-98963600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr2:98962600-98963600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:98962600-98963800	Bivalent/Poised TSS	Fetal Brain Female	brain
41	chr2:98962600-98964000	Bivalent/Poised TSS	NH-A	brain
42	chr2:98962600-98964200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr2:98962600-98964200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
44	chr2:98962600-98964200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:98962600-98964400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:98962600-98964400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
47	chr2:98962600-98964400	Bivalent Enhancer	Liver	Liver
48	chr2:98962600-98965000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
49	chr2:98962600-98965200	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:98962600-98965200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links