Variant report

Variant	rs789748
Chromosome Location	chr12:64569261-64569262
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64569180..64571134-chr12:64613693..64615934,2	K562	blood:
2	chr12:64563969..64566740-chr12:64567525..64570598,3	MCF-7	breast:
3	chr12:64566259..64570333-chr12:64574153..64576842,4	MCF-7	breast:
4	chr12:64534344..64535876-chr12:64567198..64569416,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1021665	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10748001	0.81[CEU][hapmap]
rs10748003	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10784384	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10784385	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10878110	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10878116	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10878117	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10878118	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10878126	0.81[MKK][hapmap]
rs11175269	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11175270	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1695105	1.00[ASW][hapmap];0.80[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap]
rs2643665	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3932167	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4763139	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs699633	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs722526	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs789711	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs789712	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs789713	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs789721	0.89[ASW][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap]
rs789752	0.81[CEU][hapmap]
rs9788007	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3351487	chr12:64420364-64763950	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv3509287	chr12:64526217-64736995	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3509288	chr12:64526217-64736995	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs789748	RBMS1	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64563600-64574600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:64564200-64569400	Weak transcription	Brain Angular Gyrus	brain
3	chr12:64564400-64569400	Weak transcription	Brain Anterior Caudate	brain
4	chr12:64565600-64570800	Weak transcription	HSMMtube	muscle
5	chr12:64565800-64570800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:64565800-64575200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:64566000-64570600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:64566000-64574800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:64566200-64570800	Weak transcription	NH-A	brain
10	chr12:64566600-64570400	Weak transcription	HUVEC	blood vessel
11	chr12:64566600-64570600	Weak transcription	NHLF	lung
12	chr12:64566600-64571000	Weak transcription	HSMM	muscle
13	chr12:64566600-64571600	Weak transcription	A549	lung
14	chr12:64566800-64571000	Weak transcription	HMEC	breast
15	chr12:64566800-64571400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr12:64566800-64571400	Weak transcription	NHEK	skin
17	chr12:64567000-64571000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:64567000-64571200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:64567200-64571600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:64567600-64570600	Weak transcription	Osteobl	bone
21	chr12:64567800-64569400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:64567800-64570200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:64567800-64573800	Weak transcription	Hela-S3	cervix
24	chr12:64567800-64585600	Weak transcription	Fetal Intestine Small	intestine
25	chr12:64568600-64569800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:64568600-64569800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:64568600-64574400	Weak transcription	Psoas Muscle	Psoas
28	chr12:64568600-64574800	Enhancers	NHDF-Ad	bronchial
29	chr12:64568800-64569600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:64568800-64569600	Enhancers	Fetal Brain Female	brain
31	chr12:64568800-64569800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr12:64569000-64569600	Enhancers	Fetal Brain Male	brain
33	chr12:64569000-64569800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:64569200-64569600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:64569200-64569600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:64569200-64569600	Enhancers	Adipose Nuclei	Adipose
37	chr12:64569200-64569600	Enhancers	Brain Cingulate Gyrus	brain
38	chr12:64569200-64569800	Enhancers	Brain Inferior Temporal Lobe	brain

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