Variant report

Variant	rs10400653
Chromosome Location	chr13:51504266-51504267
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	chr13:51484185..51486351-chr13:51503175..51505041,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233672	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1041017	0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs11616524	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11617366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17075018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17075030	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67932352	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73186365	1.00[ASN][1000 genomes]
rs73186367	1.00[ASN][1000 genomes]
rs73186368	1.00[ASN][1000 genomes]
rs73186369	1.00[ASN][1000 genomes]
rs73186371	1.00[ASN][1000 genomes]
rs73186372	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73186374	1.00[ASN][1000 genomes]
rs73186376	1.00[ASN][1000 genomes]
rs73186381	1.00[ASN][1000 genomes]
rs73186382	1.00[ASN][1000 genomes]
rs73186390	1.00[ASN][1000 genomes]
rs7331290	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999515	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535531	0.86[ASN][1000 genomes]
rs9535533	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535538	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900077	chr13:51446114-51514831	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51486600-51528400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr13:51489600-51508200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr13:51491600-51551000	Weak transcription	Small Intestine	intestine
4	chr13:51493800-51504800	Weak transcription	Right Ventricle	heart
5	chr13:51496600-51508200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr13:51496600-51529800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr13:51496800-51508600	Weak transcription	Fetal Kidney	kidney
8	chr13:51496800-51510600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr13:51496800-51533200	Weak transcription	NH-A	brain
10	chr13:51498400-51508600	Weak transcription	Brain Hippocampus Middle	brain
11	chr13:51499000-51508200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr13:51499000-51509000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr13:51499600-51506400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr13:51499600-51511800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr13:51500000-51506800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr13:51500000-51507200	Weak transcription	Brain Anterior Caudate	brain
17	chr13:51500200-51506600	Weak transcription	Aorta	Aorta
18	chr13:51500200-51508600	Weak transcription	Pancreas	Pancrea
19	chr13:51500400-51506600	Weak transcription	Fetal Intestine Small	intestine
20	chr13:51500600-51506800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr13:51500600-51507000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr13:51501200-51509000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr13:51501400-51504800	Weak transcription	Fetal Intestine Large	intestine
24	chr13:51501400-51508000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr13:51501400-51508200	Weak transcription	Fetal Brain Male	brain
26	chr13:51501600-51504800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr13:51501600-51506600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr13:51501600-51508800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr13:51501800-51508600	Weak transcription	A549	lung
30	chr13:51501800-51525000	Weak transcription	Brain Substantia Nigra	brain
31	chr13:51502000-51504800	Weak transcription	Liver	Liver
32	chr13:51502200-51504800	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr13:51502400-51504400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr13:51502400-51504800	Weak transcription	Lung	lung
35	chr13:51502400-51506200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr13:51502400-51508200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr13:51502400-51511800	Weak transcription	Colonic Mucosa	Colon
38	chr13:51502400-51530800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr13:51502400-51531200	Weak transcription	NHLF	lung
40	chr13:51502600-51508600	Weak transcription	HepG2	liver
41	chr13:51502600-51508800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr13:51502600-51508800	Weak transcription	Fetal Brain Female	brain
43	chr13:51502600-51509200	Weak transcription	Gastric	stomach
44	chr13:51502600-51511600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr13:51502800-51504400	Genic enhancers	Fetal Thymus	thymus
46	chr13:51502800-51504600	Weak transcription	Fetal Heart	heart
47	chr13:51502800-51508800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr13:51502800-51509000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr13:51503000-51504400	Enhancers	NHDF-Ad	bronchial
50	chr13:51503000-51504800	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links