Variant report

Variant	rs9561938
Chromosome Location	chr13:96364207-96364208
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	chr13:96356947..96358529-chr13:96362662..96364271,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12583253	0.84[ASN][1000 genomes]
rs12583374	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12585001	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12585954	0.82[ASN][1000 genomes]
rs17881101	0.84[ASN][1000 genomes]
rs17882362	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289812	1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[ASN][1000 genomes]
rs2289813	1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[ASN][1000 genomes]
rs3759446	1.00[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs3848075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4536336	0.82[CEU][hapmap]
rs4773918	0.85[CEU][hapmap]
rs58498169	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60253451	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6492811	0.82[CEU][hapmap]
rs72632666	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72632667	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336750	0.91[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap]
rs9556491	0.85[CEU][hapmap]
rs9556494	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9556498	1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[ASN][1000 genomes]
rs9561919	1.00[CEU][hapmap]
rs9561920	0.85[CEU][hapmap]
rs9561921	1.00[CEU][hapmap]
rs9561922	0.81[EUR][1000 genomes]
rs9561925	0.85[JPT][hapmap]
rs9561933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9561944	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9561950	1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[ASN][1000 genomes]
rs9561952	1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[ASN][1000 genomes]
rs9561954	0.84[ASN][1000 genomes]
rs9561958	0.84[ASN][1000 genomes]
rs9561966	0.91[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap]
rs9561970	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs9669929	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv832690	chr13:96330757-96508077	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96347000-96377600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr13:96350800-96365400	Weak transcription	HSMMtube	muscle
3	chr13:96351000-96365800	Weak transcription	Brain Anterior Caudate	brain
4	chr13:96351000-96365800	Weak transcription	Fetal Brain Male	brain
5	chr13:96351000-96368600	Weak transcription	Lung	lung
6	chr13:96354200-96364600	Weak transcription	Brain Angular Gyrus	brain
7	chr13:96355000-96364800	Weak transcription	Esophagus	oesophagus
8	chr13:96356000-96365200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr13:96356000-96372400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr13:96356600-96393600	Weak transcription	Right Ventricle	heart
11	chr13:96356800-96366000	Weak transcription	Hela-S3	cervix
12	chr13:96358800-96365600	Weak transcription	Brain Hippocampus Middle	brain
13	chr13:96359400-96386200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr13:96359800-96368000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr13:96359800-96379200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr13:96360000-96364600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr13:96360000-96364800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr13:96360200-96365600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr13:96360400-96365400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr13:96360400-96369400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr13:96360600-96364600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr13:96360600-96364600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr13:96360600-96367200	Weak transcription	Gastric	stomach
24	chr13:96360600-96379200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr13:96360600-96383000	Weak transcription	K562	blood
26	chr13:96360600-96384000	Weak transcription	Small Intestine	intestine
27	chr13:96360800-96364400	Weak transcription	HUVEC	blood vessel
28	chr13:96360800-96365200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr13:96360800-96365800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr13:96360800-96374400	Weak transcription	Colon Smooth Muscle	Colon
31	chr13:96361000-96367000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr13:96361000-96367200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr13:96361000-96368600	Weak transcription	Pancreas	Pancrea
34	chr13:96361000-96371000	Weak transcription	Aorta	Aorta
35	chr13:96361000-96380600	Weak transcription	Fetal Heart	heart
36	chr13:96361000-96393600	Weak transcription	Spleen	Spleen
37	chr13:96361200-96365200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr13:96361200-96368400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr13:96361400-96365200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr13:96361600-96364800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr13:96362000-96365400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr13:96362200-96364400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr13:96362200-96364600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr13:96362200-96364600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr13:96362200-96364600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr13:96362200-96364600	Strong transcription	Fetal Intestine Large	intestine
47	chr13:96362200-96364600	Strong transcription	NH-A	brain
48	chr13:96362200-96364800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr13:96362200-96364800	Strong transcription	Fetal Muscle Trunk	muscle
50	chr13:96362200-96364800	Strong transcription	Fetal Muscle Leg	muscle

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