Variant report

Variant	rs2643665
Chromosome Location	chr12:64580984-64580985
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64295407..64297289-chr12:64579521..64581467,2	MCF-7	breast:
2	chr12:64579699..64582531-chr12:64614447..64617129,4	MCF-7	breast:
3	chr12:64578028..64582005-chr12:64614594..64617050,4	MCF-7	breast:
4	chr12:64580918..64582549-chr12:64601522..64604143,2	K562	blood:

Variant related genes	Relation type
ENSG00000174206	Chromatin interaction
ENSG00000243024	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1021665	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10748003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10784384	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10784385	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10878110	0.83[ASN][1000 genomes]
rs10878116	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10878117	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10878118	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11175269	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11175270	0.82[ASN][1000 genomes]
rs1695105	0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs3932167	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4763139	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs699633	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs722526	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs789711	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]
rs789712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs789713	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs789721	0.84[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes]
rs789748	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs789749	0.80[AMR][1000 genomes]
rs789750	0.80[AMR][1000 genomes]
rs9788007	0.88[AMR][1000 genomes];0.87[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
rs2643665	RBMS1	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64567800-64585600	Weak transcription	Fetal Intestine Small	intestine
2	chr12:64574600-64587600	Weak transcription	Left Ventricle	heart
3	chr12:64574600-64597000	Weak transcription	Esophagus	oesophagus
4	chr12:64574800-64586400	Weak transcription	Primary T cells from cord blood	blood
5	chr12:64575000-64615200	Weak transcription	Psoas Muscle	Psoas
6	chr12:64575200-64597000	Weak transcription	Aorta	Aorta
7	chr12:64575400-64586000	Weak transcription	Ovary	ovary
8	chr12:64575400-64587600	Weak transcription	Spleen	Spleen
9	chr12:64575400-64590400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:64575600-64586200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:64575600-64586800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:64575600-64587400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:64575600-64587600	Weak transcription	Brain Angular Gyrus	brain
14	chr12:64575600-64607600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:64575600-64615000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:64575800-64615200	Weak transcription	Fetal Stomach	stomach
17	chr12:64576000-64581000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:64576000-64587400	Weak transcription	Brain Anterior Caudate	brain
19	chr12:64576000-64587600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr12:64576000-64587800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr12:64576000-64597200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:64576000-64615000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:64576200-64586600	Weak transcription	Brain Substantia Nigra	brain
24	chr12:64576200-64586800	Weak transcription	Liver	Liver
25	chr12:64576200-64587400	Weak transcription	Brain Hippocampus Middle	brain
26	chr12:64576200-64587800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:64576200-64589600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr12:64576400-64587400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:64576600-64581000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:64576600-64587400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:64579000-64586200	Weak transcription	Primary B cells from cord blood	blood
32	chr12:64580400-64581000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:64580400-64581000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr12:64580400-64581000	Enhancers	Placenta Amnion	Placenta Amnion
35	chr12:64580400-64581200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:64580400-64581200	Enhancers	HSMM	muscle
37	chr12:64580400-64581800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:64580400-64582000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:64580400-64582000	Enhancers	HMEC	breast
40	chr12:64580400-64582400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:64580400-64582400	Enhancers	NHLF	lung
42	chr12:64580400-64582600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:64580400-64582600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:64580400-64582600	Enhancers	HUVEC	blood vessel
45	chr12:64580400-64582600	Enhancers	NHDF-Ad	bronchial
46	chr12:64580600-64581200	Enhancers	HSMMtube	muscle
47	chr12:64580600-64582400	Enhancers	Osteobl	bone
48	chr12:64580600-64583400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:64580600-64583800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:64580800-64581000	Enhancers	A549	lung

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