Variant report

Variant	rs2745915
Chromosome Location	chr11:34376882-34376883
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:34352862..34355628-chr11:34375081..34377214,3	MCF-7	breast:
2	chr11:34126304..34129768-chr11:34376546..34381116,4	MCF-7	breast:
3	chr11:34195960..34197951-chr11:34375178..34377158,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135372	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs2078164	0.85[JPT][hapmap]
rs2611117	0.85[EUR][1000 genomes]
rs2611121	0.85[EUR][1000 genomes]
rs2611133	0.85[EUR][1000 genomes]
rs2611147	0.85[EUR][1000 genomes]
rs2611149	0.85[EUR][1000 genomes]
rs2611150	0.85[EUR][1000 genomes]
rs2611152	0.85[EUR][1000 genomes]
rs2745906	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs2745910	0.85[EUR][1000 genomes]
rs2745911	0.85[EUR][1000 genomes]
rs2745912	0.85[EUR][1000 genomes]
rs2745913	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2745921	0.85[EUR][1000 genomes]
rs2745922	0.85[EUR][1000 genomes]
rs2745923	0.85[EUR][1000 genomes]
rs2746152	0.85[EUR][1000 genomes]
rs2746163	0.84[EUR][1000 genomes]
rs2746164	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs2746165	0.85[EUR][1000 genomes]
rs2746166	0.85[EUR][1000 genomes]
rs2746167	0.85[EUR][1000 genomes]
rs4756137	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897205	chr11:34248229-34507213	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv897210	chr11:34349427-34381075	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2745915	RAG1	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34368400-34377800	Weak transcription	Gastric	stomach
2	chr11:34372000-34377200	Weak transcription	Aorta	Aorta
3	chr11:34375200-34377000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr11:34375400-34377400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr11:34375600-34377000	Enhancers	Brain Substantia Nigra	brain
6	chr11:34375600-34378000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:34375800-34378000	Flanking Active TSS	Brain Germinal Matrix	brain
8	chr11:34376000-34377200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:34376200-34377000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:34376200-34377000	Enhancers	Fetal Brain Male	brain
11	chr11:34376200-34377000	Enhancers	Right Ventricle	heart
12	chr11:34376200-34377000	Flanking Active TSS	HSMMtube	muscle
13	chr11:34376200-34377200	Enhancers	Brain Anterior Caudate	brain
14	chr11:34376200-34377200	Enhancers	Hela-S3	cervix
15	chr11:34376200-34377200	Enhancers	NH-A	brain
16	chr11:34376200-34377400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:34376200-34377400	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr11:34376200-34377600	Enhancers	Placenta	Placenta
19	chr11:34376200-34377600	Enhancers	HMEC	breast
20	chr11:34376200-34377800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
21	chr11:34376200-34378000	Flanking Active TSS	A549	lung
22	chr11:34376200-34378600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:34376400-34377000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:34376400-34377000	Active TSS	Brain Hippocampus Middle	brain
25	chr11:34376400-34377200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
26	chr11:34376400-34377200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
27	chr11:34376400-34377200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
28	chr11:34376400-34377200	Flanking Active TSS	GM12878-XiMat	blood
29	chr11:34376400-34377200	Enhancers	NHEK	skin
30	chr11:34376400-34377400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:34376400-34377400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr11:34376400-34377400	Enhancers	Fetal Thymus	thymus
33	chr11:34376400-34377400	Enhancers	Psoas Muscle	Psoas
34	chr11:34376400-34377600	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr11:34376400-34377600	Enhancers	Pancreas	Pancrea
36	chr11:34376400-34377600	Flanking Active TSS	HepG2	liver
37	chr11:34376400-34377800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:34376400-34378200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr11:34376400-34381200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr11:34376600-34377200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:34376600-34377200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
42	chr11:34376600-34377200	Bivalent Enhancer	Fetal Kidney	kidney
43	chr11:34376600-34377600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:34376600-34377600	Active TSS	Fetal Brain Female	brain
45	chr11:34376600-34377600	Weak transcription	Lung	lung
46	chr11:34376600-34378000	Flanking Active TSS	HSMM	muscle
47	chr11:34376600-34378800	Flanking Active TSS	Liver	Liver
48	chr11:34376800-34377000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
49	chr11:34376800-34377000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr11:34376800-34377000	Active TSS	Brain Cingulate Gyrus	brain

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