Variant report

Variant	rs3848075
Chromosome Location	chr13:96369317-96369318
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	chr13:96367268..96370251-chr13:96370563..96373311,2	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];0.95[ASN][1000 genomes]
rs12585001	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12585954	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs17881101	0.85[ASN][1000 genomes]
rs17882362	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2289812	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[ASN][1000 genomes]
rs2289813	1.00[CHB][hapmap];0.86[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]
rs4536336	0.82[CEU][hapmap]
rs4773918	0.85[CEU][hapmap]
rs58498169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60253451	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492811	0.82[CEU][hapmap]
rs72632666	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72632667	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7336750	0.91[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap]
rs9556491	0.85[CEU][hapmap]
rs9556494	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9556498	1.00[CHB][hapmap];0.86[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	0.86[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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9561938	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]
rs9561944	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9561950	1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[ASN][1000 genomes]
rs9561952	1.00[CHB][hapmap];0.90[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	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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:105 , 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	chr13:96356000-96372400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:96356600-96393600	Weak transcription	Right Ventricle	heart
4	chr13:96359400-96386200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr13:96359800-96379200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr13:96360400-96369400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr13:96360600-96379200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr13:96360600-96383000	Weak transcription	K562	blood
9	chr13:96360600-96384000	Weak transcription	Small Intestine	intestine
10	chr13:96360800-96374400	Weak transcription	Colon Smooth Muscle	Colon
11	chr13:96361000-96371000	Weak transcription	Aorta	Aorta
12	chr13:96361000-96380600	Weak transcription	Fetal Heart	heart
13	chr13:96361000-96393600	Weak transcription	Spleen	Spleen
14	chr13:96362200-96371200	Strong transcription	Primary T cells from cord blood	blood
15	chr13:96362400-96385800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr13:96362800-96393800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr13:96363200-96375600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr13:96363200-96380000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr13:96364200-96386200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr13:96364600-96384400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr13:96364600-96385400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr13:96364800-96377400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:96365400-96383800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr13:96365400-96383800	Weak transcription	Thymus	Thymus
25	chr13:96365600-96375800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr13:96365600-96384600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr13:96365800-96382600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr13:96365800-96383000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr13:96365800-96385200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr13:96366000-96371600	Strong transcription	Dnd41	blood
31	chr13:96366000-96377600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr13:96366000-96378200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr13:96366000-96382200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr13:96366200-96369600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr13:96366200-96370200	Weak transcription	Colonic Mucosa	Colon
36	chr13:96366200-96375600	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr13:96366200-96375600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr13:96366200-96375600	Weak transcription	Placenta	Placenta
39	chr13:96366200-96375800	Weak transcription	Adipose Nuclei	Adipose
40	chr13:96366200-96375800	Weak transcription	HepG2	liver
41	chr13:96366200-96379000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr13:96366200-96380400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr13:96366200-96382400	Weak transcription	HUVEC	blood vessel
44	chr13:96366200-96384000	Weak transcription	Brain Angular Gyrus	brain
45	chr13:96366200-96384200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr13:96366200-96385200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr13:96366200-96386400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr13:96366400-96371000	Weak transcription	Left Ventricle	heart
49	chr13:96366400-96375000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr13:96366400-96375600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links