Variant report

Variant	rs830708
Chromosome Location	chr16:12285103-12285104
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	chr16:12236133..12238164-chr16:12283683..12286173,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11642667	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1701111	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs1704094	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1704130	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2456272	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2968353	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs709418	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs709419	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs709420	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs709421	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs709422	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8062913	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs830696	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs830698	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs830700	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs830701	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs830704	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs830705	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs830706	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs830707	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs830709	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs830710	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs830724	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs830725	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs844224	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs844225	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853869	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs853870	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs862692	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs865533	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs866180	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs905952	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs937965	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9934120	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1052973	chr16:12188092-12307880	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv571461	chr16:12268830-12314451	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12242200-12299400	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr16:12257000-12296800	Weak transcription	Thymus	Thymus
3	chr16:12261200-12293400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr16:12261200-12293600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr16:12261400-12292400	Weak transcription	GM12878-XiMat	blood
6	chr16:12261800-12322000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr16:12263200-12287600	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr16:12271400-12293600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr16:12276800-12296800	Weak transcription	Gastric	stomach
10	chr16:12277600-12286400	Strong transcription	Primary B cells from cord blood	blood
11	chr16:12278600-12299400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr16:12279800-12297800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr16:12281200-12297000	Weak transcription	Lung	lung
14	chr16:12282800-12286800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr16:12282800-12297200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr16:12282800-12298800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr16:12282800-12305400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr16:12282800-12322600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr16:12283000-12285600	Weak transcription	Ovary	ovary
20	chr16:12283000-12289000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr16:12283000-12291600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr16:12283000-12293600	Weak transcription	Adipose Nuclei	Adipose
23	chr16:12283000-12296400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr16:12283000-12296600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr16:12283000-12298200	Weak transcription	Left Ventricle	heart
26	chr16:12283200-12286000	Weak transcription	Brain Germinal Matrix	brain
27	chr16:12283200-12286400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr16:12283200-12287200	Weak transcription	Osteobl	bone
29	chr16:12283200-12287600	Weak transcription	HepG2	liver
30	chr16:12283200-12298200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr16:12283200-12300200	Weak transcription	NHEK	skin
32	chr16:12283200-12302000	Weak transcription	NHDF-Ad	bronchial
33	chr16:12283400-12287000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr16:12283400-12287000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr16:12283400-12293000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr16:12283400-12310200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr16:12284200-12289600	Weak transcription	Esophagus	oesophagus
38	chr16:12284400-12291400	Weak transcription	Primary T cells from cord blood	blood
39	chr16:12284600-12285600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr16:12284600-12289000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr16:12284600-12295400	Weak transcription	HSMMtube	muscle
42	chr16:12284600-12296200	Weak transcription	Fetal Muscle Leg	muscle
43	chr16:12284600-12296600	Weak transcription	Spleen	Spleen
44	chr16:12284800-12297800	Weak transcription	Fetal Thymus	thymus
45	chr16:12285000-12285200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links