Variant report

Variant	rs1718188
Chromosome Location	chr12:121343893-121343894
allele	A/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	MAZ	chr12:121343764-121343990	HepG2	liver:	n/a	n/a
2	GATA2	chr12:121343801-121344133	SH-SY5Y	brain:	n/a	n/a
3	EP300	chr12:121343828-121344074	SK-N-SH_RA	brain:	n/a	n/a
4	FOS	chr12:121343714-121343997	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr12:121343681-121344108	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr12:121343514-121344122	MCF10A-Er-Src	breast:	n/a	n/a
7	GATA3	chr12:121343891-121344091	SH-SY5Y	brain:	n/a	n/a
8	MAFK	chr12:121343856-121344039	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121342121..121344461-chr12:121350958..121352582,2	K562	blood:
2	chr12:121336041..121337901-chr12:121343531..121346196,2	MCF-7	breast:

Variant related genes	Relation type
SPPL3	TF binding region
ENSG00000231313	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10774572	0.84[ASN][1000 genomes]
rs10849807	0.84[ASN][1000 genomes]
rs11065300	0.84[ASN][1000 genomes]
rs11065307	0.83[ASN][1000 genomes]
rs11065311	0.88[ASN][1000 genomes]
rs11065324	0.97[ASN][1000 genomes]
rs11065332	0.91[ASN][1000 genomes]
rs1151849	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1151859	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1151862	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1168944	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1168946	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1168948	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1168953	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1177585	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1179939	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12371178	0.83[ASN][1000 genomes]
rs12372231	0.97[ASN][1000 genomes]
rs12580949	0.84[ASN][1000 genomes]
rs12822123	0.83[ASN][1000 genomes]
rs12831094	0.84[ASN][1000 genomes]
rs1542859	0.88[ASN][1000 genomes]
rs1696357	0.97[ASN][1000 genomes]
rs1696390	0.97[ASN][1000 genomes]
rs2393716	0.89[ASN][1000 genomes]
rs2650017	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2701177	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2701184	0.98[ASN][1000 genomes]
rs34009825	0.88[ASN][1000 genomes]
rs35905305	0.87[ASN][1000 genomes]
rs3809313	0.88[ASN][1000 genomes]
rs3897746	0.88[ASN][1000 genomes]
rs4454799	0.84[ASN][1000 genomes]
rs4766980	0.84[ASN][1000 genomes]
rs4767941	0.96[ASN][1000 genomes]
rs487943	0.85[ASN][1000 genomes]
rs520753	0.85[ASN][1000 genomes]
rs533264	0.85[ASN][1000 genomes]
rs548452	0.84[ASN][1000 genomes]
rs58918988	0.87[ASN][1000 genomes]
rs602984	0.85[ASN][1000 genomes]
rs609700	0.85[ASN][1000 genomes]
rs610694	0.85[ASN][1000 genomes]
rs61946382	0.98[ASN][1000 genomes]
rs61946383	0.94[ASN][1000 genomes]
rs61946384	0.95[ASN][1000 genomes]
rs61946385	0.95[ASN][1000 genomes]
rs61946386	0.94[ASN][1000 genomes]
rs625228	0.80[EUR][1000 genomes]
rs647881	0.85[ASN][1000 genomes]
rs660549	0.86[EUR][1000 genomes]
rs665585	0.84[ASN][1000 genomes]
rs666976	0.82[ASN][1000 genomes]
rs73413868	0.84[ASN][1000 genomes]
rs73415720	0.98[ASN][1000 genomes]
rs73415734	0.94[ASN][1000 genomes]
rs7967190	0.91[ASN][1000 genomes]
rs7969140	0.84[ASN][1000 genomes]
rs7980311	0.98[ASN][1000 genomes]
rs869781	0.89[ASN][1000 genomes]
rs904628	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv560448	chr12:121341477-121364324	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv560452	chr12:121341581-121357934	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv560453	chr12:121342186-121364324	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1718188	SPPL3	cis	Adipose Subcutaneous	GTEx
rs1718188	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121342400-121345000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:121342600-121345000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:121342600-121345000	Weak transcription	Aorta	Aorta
4	chr12:121342600-121345400	Weak transcription	Lung	lung
5	chr12:121342600-121345400	Weak transcription	Right Atrium	heart
6	chr12:121342600-121345800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:121342600-121345800	Enhancers	HMEC	breast
8	chr12:121342600-121346000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:121342600-121347600	Enhancers	Placenta	Placenta
10	chr12:121342800-121344000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:121342800-121344000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:121342800-121344400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:121342800-121344800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:121342800-121344800	Weak transcription	Hela-S3	cervix
15	chr12:121342800-121345000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:121342800-121345000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:121342800-121345000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:121342800-121345000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:121342800-121345000	Weak transcription	Fetal Muscle Leg	muscle
20	chr12:121342800-121345000	Weak transcription	HSMM	muscle
21	chr12:121342800-121345000	Weak transcription	NH-A	brain
22	chr12:121342800-121345000	Weak transcription	NHDF-Ad	bronchial
23	chr12:121342800-121345000	Enhancers	NHEK	skin
24	chr12:121342800-121345000	Weak transcription	Osteobl	bone
25	chr12:121342800-121345200	Weak transcription	NHLF	lung
26	chr12:121342800-121345800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr12:121342800-121346200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:121342800-121346600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:121342800-121347000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:121342800-121347400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:121342800-121347400	Weak transcription	GM12878-XiMat	blood
32	chr12:121343000-121344800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:121343000-121344800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:121343000-121344800	Weak transcription	Fetal Heart	heart
35	chr12:121343000-121345000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr12:121343000-121362800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr12:121343200-121347200	Weak transcription	Spleen	Spleen
38	chr12:121343600-121344400	Flanking Active TSS	HepG2	liver
39	chr12:121343600-121345800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr12:121343800-121344000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:121343800-121344400	Enhancers	Psoas Muscle	Psoas
42	chr12:121343800-121345000	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr12:121343800-121347400	Enhancers	Esophagus	oesophagus

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