Variant report

Variant	rs2677283
Chromosome Location	chr16:12534623-12534624
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	chr16:12533985..12536929-chr16:12543144..12544698,2	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10251307	0.84[AFR][1000 genomes]
rs10950303	0.89[AFR][1000 genomes]
rs1232509	1.00[AMR][1000 genomes]
rs1232511	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1232518	1.00[AMR][1000 genomes]
rs2428279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2521199	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2521200	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2521202	1.00[AMR][1000 genomes]
rs2521204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2677278	1.00[AMR][1000 genomes]
rs2677280	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2677286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2944836	1.00[AFR][1000 genomes]
rs4295535	1.00[AFR][1000 genomes]
rs4442008	0.84[AFR][1000 genomes]
rs4518555	0.84[AFR][1000 genomes]
rs472164	1.00[AMR][1000 genomes]
rs472884	1.00[AMR][1000 genomes]
rs484279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs484343	0.84[AFR][1000 genomes]
rs490212	0.84[AFR][1000 genomes]
rs495774	1.00[AMR][1000 genomes]
rs498441	1.00[AFR][1000 genomes]
rs502780	1.00[AMR][1000 genomes]
rs502865	1.00[AMR][1000 genomes]
rs510451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs511253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs513388	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs523703	1.00[AMR][1000 genomes]
rs525723	1.00[AMR][1000 genomes]
rs531685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs533150	1.00[AMR][1000 genomes]
rs536128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs548750	0.84[AFR][1000 genomes]
rs550322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs563410	1.00[AFR][1000 genomes]
rs564528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs567653	0.84[AFR][1000 genomes]
rs568003	1.00[AMR][1000 genomes]
rs569837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs572043	0.84[AFR][1000 genomes]
rs573987	0.84[AFR][1000 genomes]
rs575357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs579471	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs581297	1.00[AMR][1000 genomes]
rs6460705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6460706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6460712	0.84[AFR][1000 genomes]
rs6946262	0.84[AFR][1000 genomes]
rs6948582	0.84[AFR][1000 genomes]
rs6949384	1.00[AFR][1000 genomes]
rs6969123	1.00[AFR][1000 genomes]
rs7791150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs844681	0.81[AFR][1000 genomes]
rs844683	0.81[AFR][1000 genomes]
rs844714	1.00[AFR][1000 genomes]
rs844718	0.88[AFR][1000 genomes]
rs844721	0.88[AFR][1000 genomes]
rs844726	0.88[AFR][1000 genomes]
rs844742	0.88[AFR][1000 genomes]
rs844748	0.88[AFR][1000 genomes]
rs844783	0.82[AFR][1000 genomes]
rs859999	1.00[AFR][1000 genomes]
rs860009	1.00[AFR][1000 genomes]
rs864168	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1051242	chr16:12482972-12897243	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv542749	chr16:12482972-12897243	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1035581	chr16:12516946-12863700	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1036612	chr16:12518604-12565232	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1051607	chr16:12522130-13347676	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv542750	chr16:12522130-13347676	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12497800-12539800	Weak transcription	Left Ventricle	heart
2	chr16:12498000-12541200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr16:12498400-12564600	Weak transcription	Esophagus	oesophagus
4	chr16:12511400-12552000	Weak transcription	Lung	lung
5	chr16:12513200-12536600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr16:12517000-12550800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr16:12517400-12537000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr16:12517400-12537000	Weak transcription	Aorta	Aorta
9	chr16:12518400-12537000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr16:12522000-12537600	Weak transcription	Primary B cells from cord blood	blood
11	chr16:12524000-12536800	Weak transcription	Primary T cells from cord blood	blood
12	chr16:12524000-12551400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr16:12527800-12536800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr16:12528600-12537800	Weak transcription	Fetal Lung	lung
15	chr16:12528800-12564400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr16:12529800-12544400	Weak transcription	Gastric	stomach
17	chr16:12530400-12577600	Weak transcription	Pancreas	Pancrea
18	chr16:12531600-12552000	Weak transcription	Spleen	Spleen
19	chr16:12531800-12540600	Weak transcription	Liver	Liver
20	chr16:12531800-12544400	Weak transcription	Ovary	ovary
21	chr16:12531800-12552000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr16:12532000-12545800	Weak transcription	Brain Hippocampus Middle	brain
23	chr16:12532200-12543000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr16:12532400-12543400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr16:12532400-12545800	Weak transcription	Brain Anterior Caudate	brain
26	chr16:12532400-12552000	Weak transcription	Thymus	Thymus
27	chr16:12533800-12536400	Weak transcription	GM12878-XiMat	blood
28	chr16:12534000-12536000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr16:12534000-12536000	Weak transcription	Brain Substantia Nigra	brain
30	chr16:12534000-12537400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr16:12534000-12545800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr16:12534000-12552000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr16:12534000-12556000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr16:12534200-12544000	Weak transcription	HSMM	muscle
35	chr16:12534200-12549000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr16:12534400-12534800	ZNF genes & repeats	Adipose Nuclei	Adipose
37	chr16:12534400-12539000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr16:12534400-12541800	Weak transcription	Placenta	Placenta
39	chr16:12534400-12552000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr16:12534600-12537400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr16:12534600-12543200	Weak transcription	HSMMtube	muscle
42	chr16:12534600-12545200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr16:12534600-12545800	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links