Variant report

Variant	rs3782137
Chromosome Location	chr12:11916325-11916326
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:11915800..11917603-chr12:11959606..11961755,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10772505	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs11054443	0.85[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs11615083	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12425912	0.86[ASN][1000 genomes]
rs1547393	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17210559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2051524	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs2723829	0.82[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.88[ASN][1000 genomes]
rs3825082	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4763723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7310017	1.00[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs928950	0.92[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
2	nsv1053609	chr12:11898099-11933906	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv469113	chr12:11913360-11931259	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv557574	chr12:11913360-11931259	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3782137	KIAA1467	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11904000-11918000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:11905800-11918400	Weak transcription	Fetal Brain Male	brain
3	chr12:11906400-11918600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:11907000-11917200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:11907600-11918200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:11908000-11918800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:11908200-11918800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:11908600-11931800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:11909200-11919400	Weak transcription	Liver	Liver
10	chr12:11909400-11916600	Weak transcription	NHDF-Ad	bronchial
11	chr12:11909600-11932400	Genic enhancers	Fetal Thymus	thymus
12	chr12:11909800-11919000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:11910600-11916800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr12:11912000-11916600	Weak transcription	Fetal Kidney	kidney
15	chr12:11912000-11917600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr12:11912000-11918600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:11912400-11916400	Weak transcription	Fetal Lung	lung
18	chr12:11912400-11918800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:11912400-11918800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:11912400-11918800	Weak transcription	Ovary	ovary
21	chr12:11912800-11916600	Weak transcription	NHLF	lung
22	chr12:11913000-11918000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr12:11913400-11919000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:11914200-11916400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:11914200-11918000	Genic enhancers	Primary hematopoietic stem cells	blood
26	chr12:11914200-11919000	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr12:11914200-11919800	Enhancers	Brain Anterior Caudate	brain
28	chr12:11914400-11916400	Enhancers	Brain Cingulate Gyrus	brain
29	chr12:11914400-11917000	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr12:11914400-11917200	Enhancers	Brain Substantia Nigra	brain
31	chr12:11914400-11918600	Enhancers	Stomach Smooth Muscle	stomach
32	chr12:11914400-11918800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr12:11914400-11918800	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr12:11914400-11918800	Enhancers	Rectal Smooth Muscle	rectum
35	chr12:11914400-11919200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr12:11914400-11921600	Enhancers	Primary B cells from peripheral blood	blood
37	chr12:11914400-11925400	Genic enhancers	Dnd41	blood
38	chr12:11914400-11925800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:11914600-11916600	Enhancers	HSMMtube	muscle
40	chr12:11914600-11916800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr12:11914600-11917600	Enhancers	Brain Angular Gyrus	brain
42	chr12:11914600-11917600	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr12:11914600-11918000	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr12:11914600-11918000	Enhancers	Fetal Intestine Large	intestine
45	chr12:11914600-11918800	Enhancers	Small Intestine	intestine
46	chr12:11914600-11920400	Enhancers	Fetal Stomach	stomach
47	chr12:11914800-11916400	Enhancers	Thymus	Thymus
48	chr12:11914800-11916600	Enhancers	Fetal Heart	heart
49	chr12:11914800-11917200	Enhancers	HSMM	muscle
50	chr12:11914800-11918600	Enhancers	Primary B cells from cord blood	blood

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