Variant report

Variant	rs789711
Chromosome Location	chr12:64573359-64573360
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64236487..64240653-chr12:64573099..64577184,5	MCF-7	breast:
2	chr12:64569573..64573901-chr12:64574064..64577068,4	K562	blood:
3	chr12:64573179..64575576-chr7:155001263..155003585,2	MCF-7	breast:
4	chr12:64570311..64573993-chr12:64574949..64576948,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196935	Chromatin interaction

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

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

rs_ID	r²[population]
rs1021665	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10748003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10784384	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10784385	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10878110	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10878116	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10878117	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10878118	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10878126	0.85[MKK][hapmap];0.88[YRI][hapmap]
rs11175269	0.96[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11175270	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1464055	0.89[YRI][hapmap]
rs1695105	0.88[ASW][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap]
rs2643665	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3932167	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4763139	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs699633	0.96[CEU][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs722526	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs789712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs789713	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs789721	1.00[ASW][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs789748	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs789749	0.85[YRI][hapmap]
rs9788007	0.85[AMR][1000 genomes];0.84[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
rs789711	RBMS1	cis	cerebellum	SCAN

Chromatin state (count:41 , 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	chr12:64565800-64575200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:64566000-64574800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:64567800-64573800	Weak transcription	Hela-S3	cervix
5	chr12:64567800-64585600	Weak transcription	Fetal Intestine Small	intestine
6	chr12:64568600-64574400	Weak transcription	Psoas Muscle	Psoas
7	chr12:64568600-64574800	Enhancers	NHDF-Ad	bronchial
8	chr12:64569600-64574200	Weak transcription	Adipose Nuclei	Adipose
9	chr12:64569600-64574400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:64569600-64574800	Weak transcription	Brain Anterior Caudate	brain
11	chr12:64569600-64575200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:64569800-64574400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:64569800-64575200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:64569800-64575200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:64569800-64575200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr12:64570200-64578400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:64570600-64575000	Enhancers	Osteobl	bone
18	chr12:64570600-64576200	Enhancers	NHLF	lung
19	chr12:64570800-64573400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:64570800-64574800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:64570800-64575800	Enhancers	NH-A	brain
22	chr12:64571000-64573400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:64571200-64574400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:64571400-64573600	Enhancers	NHEK	skin
25	chr12:64571400-64575800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr12:64571800-64573800	Weak transcription	Spleen	Spleen
27	chr12:64571800-64575200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:64571800-64575600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:64572200-64574200	Weak transcription	Fetal Lung	lung
30	chr12:64572600-64573800	Weak transcription	HSMM	muscle
31	chr12:64572600-64574000	Weak transcription	A549	lung
32	chr12:64572600-64574400	Weak transcription	HSMMtube	muscle
33	chr12:64572800-64574000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:64572800-64575200	Weak transcription	Fetal Heart	heart
35	chr12:64572800-64575800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:64573000-64573800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:64573000-64575200	Weak transcription	Ovary	ovary
38	chr12:64573200-64573600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:64573200-64573600	Weak transcription	HUVEC	blood vessel
40	chr12:64573200-64573800	Weak transcription	HMEC	breast
41	chr12:64573200-64574400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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