Variant report

Variant	rs2897770
Chromosome Location	chr13:50325070-50325071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50318990..50321781-chr13:50323310..50326144,3	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1009333	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10492591	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1127021	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1198315	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1198319	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1198320	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1198322	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1198324	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1201716	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1211304	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1407440	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1407441	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1547623	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1570353	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1581745	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2025263	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2181185	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2407804	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3851162	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4942863	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61961491	0.88[AMR][1000 genomes]
rs61961501	0.80[AMR][1000 genomes]
rs7330392	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7983303	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7984061	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9316474	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9526591	0.93[EUR][1000 genomes]
rs9526593	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9535305	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9535307	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9535310	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9535316	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9535330	0.80[EUR][1000 genomes]
rs9535340	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9535341	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9562927	0.90[AMR][1000 genomes];0.83[EUR][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	nsv900072	chr13:50266109-50381016	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv900073	chr13:50286218-50381016	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv1818134	chr13:50306897-50374102	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv900074	chr13:50317104-50381016	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1038	chr13:50324773-50359990	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2897770	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs2897770	KPNA3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
2	chr13:50273200-50326000	Weak transcription	Aorta	Aorta
3	chr13:50273200-50333800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:50290000-50334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr13:50293200-50326000	Weak transcription	Fetal Brain Male	brain
6	chr13:50294400-50333000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr13:50296200-50330400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr13:50296600-50330400	Weak transcription	Small Intestine	intestine
9	chr13:50296600-50338600	Weak transcription	Ovary	ovary
10	chr13:50298000-50327600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:50299200-50327600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr13:50300600-50345600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr13:50301200-50327800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr13:50302800-50333800	Weak transcription	Thymus	Thymus
15	chr13:50303200-50334000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr13:50306000-50351600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr13:50306200-50334200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr13:50306200-50336200	Weak transcription	Adipose Nuclei	Adipose
19	chr13:50306800-50333800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr13:50308000-50356000	Weak transcription	Fetal Kidney	kidney
21	chr13:50308200-50327400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr13:50308200-50327600	Weak transcription	Lung	lung
23	chr13:50314800-50327600	Weak transcription	Gastric	stomach
24	chr13:50315200-50336000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr13:50317600-50343600	Weak transcription	Primary T cells from cord blood	blood
26	chr13:50318800-50333800	Weak transcription	NH-A	brain
27	chr13:50319600-50333600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr13:50319600-50334800	Weak transcription	Fetal Lung	lung
29	chr13:50320000-50333600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr13:50320000-50333600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr13:50320000-50333600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr13:50320200-50327600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr13:50320400-50325800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr13:50320400-50336800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr13:50320600-50325600	Weak transcription	Spleen	Spleen
36	chr13:50320600-50326200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr13:50320600-50327600	Weak transcription	Liver	Liver
38	chr13:50320600-50327600	Weak transcription	Pancreas	Pancrea
39	chr13:50320600-50327800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr13:50320600-50332200	Weak transcription	Fetal Muscle Leg	muscle
41	chr13:50320600-50332600	Weak transcription	Fetal Brain Female	brain
42	chr13:50320600-50333000	Weak transcription	Fetal Intestine Large	intestine
43	chr13:50320600-50333600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr13:50320600-50333600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr13:50320600-50333600	Weak transcription	Fetal Intestine Small	intestine
46	chr13:50320600-50333800	Weak transcription	Brain Hippocampus Middle	brain
47	chr13:50320600-50333800	Weak transcription	Fetal Stomach	stomach
48	chr13:50320600-50334800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr13:50320600-50334800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr13:50320600-50337400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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