Variant report

Variant	rs1255992
Chromosome Location	chr14:64662895-64662896
allele	A/G
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	chr14:64662665-64665717	H1-neurons	neurons:	n/a	chr14:64663684-64663704 chr14:64663869-64663878 chr14:64663684-64663704 chr14:64663684-64663704 chr14:64663726-64663739
2	MYC	chr14:64662676-64663002	K562	blood:	n/a	chr14:64662822-64662832 chr14:64662818-64662833 chr14:64662821-64662832 chr14:64662897-64662906 chr14:64662822-64662831 chr14:64662821-64662830 chr14:64662896-64662907 chr14:64662895-64662908 chr14:64662821-64662831 chr14:64662820-64662830 chr14:64662899-64662906 chr14:64662820-64662835 chr14:64662896-64662907 chr14:64662822-64662832 chr14:64662896-64662907 chr14:64662820-64662833 chr14:64662824-64662833 chr14:64662821-64662832 chr14:64662899-64662915
3	MXI1	chr14:64662608-64664261	IMR90	lung:	n/a	chr14:64662823-64662832 chr14:64662821-64662830
4	MAX	chr14:64662786-64662986	NB4	blood:	n/a	chr14:64662822-64662832 chr14:64662818-64662833 chr14:64662821-64662832 chr14:64662897-64662906 chr14:64662822-64662831 chr14:64662821-64662830 chr14:64662896-64662907 chr14:64662895-64662908 chr14:64662821-64662831 chr14:64662820-64662830 chr14:64662899-64662906 chr14:64662820-64662835 chr14:64662896-64662907 chr14:64662822-64662832 chr14:64662896-64662907 chr14:64662820-64662833 chr14:64662824-64662833 chr14:64662821-64662832 chr14:64662899-64662915
5	MAX	chr14:64662654-64663017	K562	blood:	n/a	chr14:64662822-64662832 chr14:64662818-64662833 chr14:64662821-64662832 chr14:64662897-64662906 chr14:64662822-64662831 chr14:64662821-64662830 chr14:64662896-64662907 chr14:64662895-64662908 chr14:64662821-64662831 chr14:64662820-64662830 chr14:64662899-64662906 chr14:64662820-64662835 chr14:64662896-64662907 chr14:64662822-64662832 chr14:64662896-64662907 chr14:64662820-64662833 chr14:64662824-64662833 chr14:64662821-64662832 chr14:64662899-64662915
6	POLR2A	chr14:64661633-64662948	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64662559..64666637-chr14:64681435..64684914,4	MCF-7	breast:

Variant related genes	Relation type
SYNE2	TF binding region
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1152590	0.83[AMR][1000 genomes]
rs1152592	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1152593	0.81[AMR][1000 genomes]
rs1152594	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1152595	0.84[AFR][1000 genomes]
rs1152601	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1255984	0.94[ASN][1000 genomes]
rs1255986	0.89[ASN][1000 genomes]
rs1255988	0.88[ASN][1000 genomes]
rs1255990	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1255991	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1262242	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1266927	0.92[ASN][1000 genomes]
rs1272715	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2027094	0.80[EUR][1000 genomes]
rs2781379	0.83[EUR][1000 genomes]
rs872227	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv456326	chr14:64420413-64754361	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv564905	chr14:64420413-64754361	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv902021	chr14:64647646-64715794	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1255992	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs1255992	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs1255992	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs1255992	SYNE2	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64600600-64667400	Weak transcription	Stomach Mucosa	stomach
2	chr14:64637400-64663600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr14:64640000-64663400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr14:64645800-64663600	Weak transcription	Colonic Mucosa	Colon
5	chr14:64650800-64663200	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr14:64650800-64671800	Strong transcription	Liver	Liver
7	chr14:64652800-64666200	Strong transcription	Dnd41	blood
8	chr14:64653000-64664000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr14:64653600-64663400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr14:64655800-64663400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr14:64655800-64663600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr14:64656400-64663400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr14:64657600-64663400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr14:64657600-64663400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr14:64657800-64663600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr14:64658200-64663200	Weak transcription	Thymus	Thymus
17	chr14:64658200-64667000	Weak transcription	Esophagus	oesophagus
18	chr14:64658600-64663200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr14:64659200-64663400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr14:64659200-64663400	Weak transcription	NH-A	brain
21	chr14:64659200-64663400	Weak transcription	NHLF	lung
22	chr14:64659200-64663600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr14:64659600-64663400	Weak transcription	HMEC	breast
24	chr14:64659800-64663600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr14:64660000-64663000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr14:64660000-64663200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr14:64660000-64663400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr14:64660000-64663600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr14:64660000-64663800	Weak transcription	Aorta	Aorta
30	chr14:64660200-64663400	Weak transcription	Adipose Nuclei	Adipose
31	chr14:64660200-64663400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr14:64660200-64663400	Weak transcription	Fetal Stomach	stomach
33	chr14:64660400-64663400	Enhancers	Fetal Heart	heart
34	chr14:64660400-64663400	Weak transcription	Fetal Muscle Leg	muscle
35	chr14:64660400-64663600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr14:64660400-64664400	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr14:64660600-64665200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr14:64660800-64663400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr14:64660800-64682600	Weak transcription	Hela-S3	cervix
40	chr14:64661000-64663000	Enhancers	K562	blood
41	chr14:64661000-64663200	Genic enhancers	Primary T cells fromperipheralblood	blood
42	chr14:64661000-64663200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr14:64661000-64663400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr14:64661000-64663400	Enhancers	Primary B cells from cord blood	blood
45	chr14:64661000-64663600	Enhancers	Pancreas	Pancrea
46	chr14:64661000-64663800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr14:64661200-64663200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr14:64661200-64663200	Enhancers	Ovary	ovary
49	chr14:64661200-64663400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr14:64661200-64663600	Enhancers	Primary T helper cells fromperipheralblood	blood

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