Variant report

Variant	rs12090153
Chromosome Location	chr1:47901300-47901301
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	ZNF384	chr1:47901028-47901348	K562	blood:	n/a	n/a
2	ZNF384	chr1:47900987-47901615	GM12878	blood:	n/a	n/a
3	CTCF	chr1:47901200-47901350	AG04450	lung:	n/a	n/a
4	CTCF	chr1:47901160-47901310	HEK293	kidney:	n/a	n/a
5	CTCF	chr1:47901160-47901310	HCFaa	heart:	n/a	n/a

Variant related genes	Relation type
FOXD2-AS1	TF binding region
FOXD2	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10399673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11211503	1.00[YRI][hapmap]
rs12070024	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12090346	1.00[YRI][hapmap]
rs1316443	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1680020	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2405922	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622909	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2622917	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622920	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622921	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2820970	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2820971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2820974	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3122618	1.00[YRI][hapmap]
rs3738315	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4603175	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs505399	0.85[AMR][1000 genomes]
rs524158	0.85[AMR][1000 genomes]
rs527551	0.82[AMR][1000 genomes]
rs538286	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55718554	0.84[EUR][1000 genomes]
rs557851	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs571281	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61103903	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6673882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6673934	0.83[EUR][1000 genomes]
rs7525184	0.81[GIH][hapmap]
rs7532785	1.00[YRI][hapmap]
rs7552140	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9436412	1.00[YRI][hapmap]
rs9436883	1.00[YRI][hapmap]
rs9436899	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871961	chr1:47875627-47912628	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534956	chr1:47882277-47905486	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv534957	chr1:47882277-47907965	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1001779	chr1:47884229-48111485	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv871299	chr1:47889417-48057890	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12090153	CMPK1	cis	lymphoblastoid	seeQTL
rs12090153	CMPK1	cis	parietal	SCAN
rs12090153	CYP4Z2P	cis	cerebellum	SCAN
rs12090153	CMPK	Cis_1M	lymphoblastoid	RTeQTL
rs12090153	CYP4Z2P	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47894400-47901600	Weak transcription	HepG2	liver
2	chr1:47897000-47901600	Weak transcription	A549	lung
3	chr1:47898800-47901400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:47898800-47901600	Weak transcription	K562	blood
5	chr1:47898800-47902000	Weak transcription	HSMM	muscle
6	chr1:47898800-47902000	Weak transcription	HSMMtube	muscle
7	chr1:47899000-47901400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:47899000-47904400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:47899200-47901800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:47899200-47902200	Weak transcription	Gastric	stomach
11	chr1:47899400-47901600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:47899400-47901600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:47899800-47901800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:47900000-47902000	Enhancers	Aorta	Aorta
15	chr1:47900400-47901600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:47900400-47901600	Weak transcription	Liver	Liver
17	chr1:47900400-47901800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:47900400-47901800	Enhancers	HMEC	breast
19	chr1:47900400-47902000	Active TSS	Colonic Mucosa	Colon
20	chr1:47900400-47902200	Weak transcription	Lung	lung
21	chr1:47900400-47902200	Weak transcription	Pancreas	Pancrea
22	chr1:47900400-47902200	Weak transcription	Right Atrium	heart
23	chr1:47900600-47901800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:47900600-47902000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr1:47900600-47902000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:47900800-47901800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:47900800-47902000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:47900800-47902000	Bivalent Enhancer	NHEK	skin
29	chr1:47900800-47902000	Weak transcription	NHLF	lung
30	chr1:47901000-47901400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:47901000-47901400	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr1:47901000-47901400	Weak transcription	Spleen	Spleen
33	chr1:47901000-47901400	Weak transcription	GM12878-XiMat	blood
34	chr1:47901000-47901600	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr1:47901200-47901400	Enhancers	Hela-S3	cervix
36	chr1:47901200-47901600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr1:47901200-47902000	Transcr. at gene 5' and 3'	Dnd41	blood

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