Variant report

Variant	rs2407616
Chromosome Location	chr13:50000974-50000975
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	chr13:49994580..49997137-chr13:49999140..50001619,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102547	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs9535241	0.91[CHD][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv430558	chr13:49914393-50059354	Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv430559	chr13:49930369-50059354	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430560	chr13:49930643-50059354	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv430562	chr13:49930643-50067246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv430561	chr13:49930643-50089844	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv430564	chr13:49945247-50059354	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv430566	chr13:49945247-50089844	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv430571	chr13:49961137-50059354	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv430570	chr13:49961137-50089844	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv1807924	chr13:49991885-50036730	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv1796315	chr13:49992988-50031868	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2407616	EBPL	cis	parietal	SCAN
rs2407616	SETDB2	cis	cerebellum	SCAN
rs2407616	CAB39L	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49975600-50001000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:49975800-50001600	Weak transcription	Fetal Stomach	stomach
3	chr13:49975800-50013600	Weak transcription	Primary B cells from cord blood	blood
4	chr13:49978400-50005400	Weak transcription	Aorta	Aorta
5	chr13:49978400-50016800	Weak transcription	Fetal Brain Male	brain
6	chr13:49980400-50006400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr13:49983400-50017000	Weak transcription	Brain Anterior Caudate	brain
8	chr13:49983400-50017400	Weak transcription	Lung	lung
9	chr13:49983600-50017000	Weak transcription	Brain Angular Gyrus	brain
10	chr13:49984400-50001200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr13:49984400-50010200	Weak transcription	Brain Substantia Nigra	brain
12	chr13:49985000-50001200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr13:49989200-50006800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr13:49993800-50001600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr13:49993800-50017400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr13:49994000-50002000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr13:49994000-50010000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr13:49994000-50010000	Weak transcription	Osteobl	bone
19	chr13:49994000-50016200	Weak transcription	NHLF	lung
20	chr13:49994000-50017000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr13:49994000-50017200	Weak transcription	HSMM	muscle
22	chr13:49994200-50001000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr13:49994200-50001200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr13:49994200-50010000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr13:49994200-50010200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr13:49994200-50017200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr13:49994600-50002200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr13:49994600-50016000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr13:49994800-50001000	Weak transcription	HSMMtube	muscle
30	chr13:49994800-50002600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr13:49994800-50017200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr13:49995400-50017000	Weak transcription	Liver	Liver
33	chr13:49995600-50017000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr13:49995800-50001800	Weak transcription	Fetal Muscle Leg	muscle
35	chr13:49995800-50007000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr13:49995800-50017000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr13:49996000-50002400	Weak transcription	Ovary	ovary
38	chr13:49996400-50010200	Weak transcription	Brain Hippocampus Middle	brain
39	chr13:49996600-50002000	Weak transcription	Primary T cells from cord blood	blood
40	chr13:49996800-50006600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr13:49997000-50017000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr13:49997000-50017200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr13:49997400-50002800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr13:49997400-50017200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr13:49998400-50007200	Weak transcription	NHDF-Ad	bronchial
46	chr13:49998600-50001400	Weak transcription	Left Ventricle	heart
47	chr13:49998600-50017000	Weak transcription	Adipose Nuclei	Adipose
48	chr13:49999000-50017400	Weak transcription	Small Intestine	intestine
49	chr13:49999800-50002600	Strong transcription	Fetal Brain Female	brain
50	chr13:50000000-50013400	Weak transcription	Primary B cells from peripheral blood	blood

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