Variant report

Variant	rs12492409
Chromosome Location	chr3:177650442-177650443
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	NFIC	chr3:177650390-177651257	SK-N-SH	brain:	n/a	n/a
2	EP300	chr3:177650294-177653620	SK-N-SH	brain:	n/a	chr3:177650794-177650808 chr3:177650435-177650449
3	EP300	chr3:177650186-177651251	SK-N-SH	brain:	n/a	chr3:177650794-177650808 chr3:177650435-177650449
4	GATA3	chr3:177650048-177651371	SK-N-SH	brain:	n/a	chr3:177650753-177650770 chr3:177650913-177650925
5	CEBPB	chr3:177650168-177650574	A549	lung:	n/a	chr3:177650322-177650334
6	FOS	chr3:177650273-177651057	HUVEC	blood vessel:	n/a	n/a
7	TCF12	chr3:177650425-177653435	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr3:177650069-177651313	SK-N-SH	brain:	n/a	chr3:177650753-177650770 chr3:177650913-177650925
9	GATA2	chr3:177650283-177651227	HUVEC	blood vessel:	n/a	chr3:177650753-177650770 chr3:177650913-177650925

Variant related genes	Relation type
ENSG00000225790	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1075544	0.80[ASN][1000 genomes]
rs10936960	0.80[ASN][1000 genomes]
rs11919677	0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11920776	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11922170	0.81[ASN][1000 genomes]
rs12489750	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492069	0.98[ASN][1000 genomes]
rs12496207	0.81[ASN][1000 genomes]
rs12497387	0.95[ASN][1000 genomes]
rs13062823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066104	0.80[ASN][1000 genomes]
rs13074448	0.83[ASN][1000 genomes]
rs13075342	0.94[ASN][1000 genomes]
rs1421157	0.80[ASN][1000 genomes]
rs1421158	0.80[ASN][1000 genomes]
rs1421160	0.80[ASN][1000 genomes]
rs1421161	0.80[ASN][1000 genomes]
rs1421162	0.80[ASN][1000 genomes]
rs1421163	0.92[ASN][1000 genomes]
rs1421164	0.91[ASN][1000 genomes]
rs1421169	0.97[ASN][1000 genomes]
rs1421170	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1421173	0.80[ASN][1000 genomes]
rs1582399	0.87[ASN][1000 genomes]
rs16828811	0.86[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs16828819	0.95[ASN][1000 genomes]
rs1861886	0.98[ASN][1000 genomes]
rs1895068	0.80[ASN][1000 genomes]
rs1895075	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34300091	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34534264	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34603970	0.82[ASN][1000 genomes]
rs34969108	0.99[ASN][1000 genomes]
rs35494413	0.99[ASN][1000 genomes]
rs35569214	0.99[ASN][1000 genomes]
rs35751119	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3978728	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57315928	0.80[ASN][1000 genomes]
rs6769109	0.80[ASN][1000 genomes]
rs6779965	0.82[EUR][1000 genomes]
rs6786110	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6804905	0.80[ASN][1000 genomes]
rs737553	0.80[ASN][1000 genomes]
rs7616735	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7619802	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs7648771	0.81[EUR][1000 genomes]
rs9838142	0.80[ASN][1000 genomes]
rs9862300	0.80[ASN][1000 genomes]
rs9875424	0.80[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931055	chr3:177229521-177889872	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12492409	ATP11B	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:177645600-177652000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:177646400-177651000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:177646800-177652000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:177647200-177651200	Weak transcription	HSMMtube	muscle
5	chr3:177648000-177652400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:177648000-177652400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr3:177648200-177650800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:177648200-177655000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:177648400-177652800	Enhancers	Osteobl	bone
10	chr3:177648400-177653000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:177648600-177651800	Weak transcription	Fetal Heart	heart
12	chr3:177648600-177652400	Enhancers	Brain Germinal Matrix	brain
13	chr3:177648600-177652600	Enhancers	HSMM	muscle
14	chr3:177648600-177652600	Enhancers	NHDF-Ad	bronchial
15	chr3:177648800-177650800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:177648800-177652600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:177649000-177652200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:177649200-177651200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:177649200-177651200	Weak transcription	NHLF	lung
20	chr3:177649200-177651800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:177649200-177652600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:177649200-177657000	Weak transcription	Esophagus	oesophagus
23	chr3:177649400-177651400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:177649600-177652400	Enhancers	HUVEC	blood vessel
25	chr3:177649800-177652000	Enhancers	A549	lung
26	chr3:177649800-177652400	Enhancers	NH-A	brain
27	chr3:177649800-177654200	Enhancers	Primary hematopoietic stem cells	blood
28	chr3:177650000-177652000	Weak transcription	Psoas Muscle	Psoas
29	chr3:177650000-177652200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:177650000-177652600	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr3:177650200-177651000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:177650200-177651000	Enhancers	Brain Angular Gyrus	brain
33	chr3:177650200-177653400	Enhancers	Fetal Lung	lung
34	chr3:177650400-177651200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:177650400-177651400	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr3:177650400-177651400	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr3:177650400-177651800	Weak transcription	Adipose Nuclei	Adipose
38	chr3:177650400-177652000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:177650400-177652000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:177650400-177652000	Weak transcription	Right Atrium	heart
41	chr3:177650400-177653000	Weak transcription	Spleen	Spleen

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