Variant report

Variant	rs2856339
Chromosome Location	chr12:11906819-11906820
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	chr12:11800154..11802196-chr12:11905804..11907326,2	MCF-7	breast:

Extended variants
information (count: 4 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs16907207	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[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	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	nsv976578	chr12:11906375-11907311	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2856339	BTG2	trans	brain	seeQTL
rs2856339	KLF4	trans	brain	seeQTL
rs2856339	FOS	trans	brain	seeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11873200-11909400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:11885800-11911600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr12:11893200-11915000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr12:11894600-11908400	Weak transcription	Psoas Muscle	Psoas
5	chr12:11895000-11912600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:11895400-11914400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr12:11895600-11908800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:11897000-11908800	Weak transcription	Brain Anterior Caudate	brain
9	chr12:11899400-11908000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:11899400-11908200	Weak transcription	HSMMtube	muscle
11	chr12:11899400-11908400	Weak transcription	HSMM	muscle
12	chr12:11900000-11907000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr12:11900400-11910600	Weak transcription	Colonic Mucosa	Colon
14	chr12:11900600-11915000	Weak transcription	NHEK	skin
15	chr12:11901400-11911000	Weak transcription	Fetal Lung	lung
16	chr12:11902800-11910600	Weak transcription	Brain Angular Gyrus	brain
17	chr12:11902800-11910600	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:11902800-11910600	Weak transcription	Brain Substantia Nigra	brain
19	chr12:11903200-11910200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:11903400-11910400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:11904000-11907000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:11904000-11908600	Genic enhancers	Fetal Thymus	thymus
23	chr12:11904000-11918000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:11904200-11907000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr12:11904200-11907000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:11904200-11913000	Strong transcription	Dnd41	blood
27	chr12:11904400-11910600	Genic enhancers	GM12878-XiMat	blood
28	chr12:11905200-11907200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:11905200-11907200	Strong transcription	Fetal Intestine Small	intestine
30	chr12:11905200-11907200	Genic enhancers	Placenta	Placenta
31	chr12:11905200-11907200	Genic enhancers	Left Ventricle	heart
32	chr12:11905200-11908000	Weak transcription	Small Intestine	intestine
33	chr12:11905200-11908000	Genic enhancers	Thymus	Thymus
34	chr12:11905200-11908400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:11905200-11908600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:11905200-11908600	Strong transcription	Fetal Intestine Large	intestine
37	chr12:11905200-11909600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr12:11905200-11910400	Strong transcription	Fetal Stomach	stomach
39	chr12:11905200-11911400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr12:11905400-11907400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr12:11905400-11907600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr12:11905400-11907800	Enhancers	Aorta	Aorta
43	chr12:11905400-11910800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr12:11905400-11911600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr12:11905600-11909600	Strong transcription	Primary T cells from cord blood	blood
46	chr12:11905600-11909600	Strong transcription	Lung	lung
47	chr12:11905800-11918400	Weak transcription	Fetal Brain Male	brain
48	chr12:11906000-11907000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:11906000-11907200	Genic enhancers	Rectal Smooth Muscle	rectum
50	chr12:11906000-11908600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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