Variant report

Variant	rs16939680
Chromosome Location	chr18:12596074-12596075
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12595958..12597985-chr18:12607168..12608800,2	MCF-7	breast:
2	chr18:12589977..12591676-chr18:12594280..12596614,2	MCF-7	breast:
3	chr18:12594070..12599084-chr18:12599553..12605396,7	K562	blood:
4	chr18:12578174..12579861-chr18:12594469..12596151,2	K562	blood:
5	chr18:12590720..12592550-chr18:12594454..12597445,2	MCF-7	breast:
6	chr18:12595174..12598244-chr18:12625042..12627627,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1539813	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs1785308	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1833326	0.83[ASN][1000 genomes]
rs1893212	0.93[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs1893213	0.80[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap]
rs2015197	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2249830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2542172	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2542174	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2847272	0.80[ASN][1000 genomes]
rs2847305	0.83[ASN][1000 genomes]
rs4796966	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4797698	0.83[ASN][1000 genomes]
rs4797701	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs479860	0.89[CEU][hapmap];0.93[CHB][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs507868	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs514831	0.89[CEU][hapmap];0.93[CHB][hapmap];0.93[MEX][hapmap]
rs56063272	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56328751	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs575093	0.89[CEU][hapmap];0.93[CHB][hapmap]
rs58135011	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60876158	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61542301	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61635631	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62095972	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62097130	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62097132	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62097145	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8086774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs8089003	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9635805	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12587800-12596800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr18:12589600-12597000	Weak transcription	Aorta	Aorta
3	chr18:12589800-12597200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr18:12589800-12597200	Weak transcription	Ovary	ovary
5	chr18:12589800-12597400	Weak transcription	Brain Angular Gyrus	brain
6	chr18:12590000-12597400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr18:12590800-12597200	Weak transcription	Fetal Brain Male	brain
8	chr18:12590800-12597800	Weak transcription	Pancreas	Pancrea
9	chr18:12590800-12599200	Weak transcription	Liver	Liver
10	chr18:12591200-12596800	Weak transcription	Fetal Brain Female	brain
11	chr18:12591400-12596800	Weak transcription	Left Ventricle	heart
12	chr18:12591400-12596800	Weak transcription	Right Atrium	heart
13	chr18:12592400-12597600	Weak transcription	Colon Smooth Muscle	Colon
14	chr18:12592800-12597800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr18:12593000-12596800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr18:12594200-12597600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr18:12594400-12596800	Weak transcription	Osteobl	bone
18	chr18:12594600-12600400	Enhancers	HepG2	liver
19	chr18:12594800-12596200	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr18:12595400-12596800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr18:12595400-12597000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr18:12595400-12597000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr18:12595400-12597200	Enhancers	HSMMtube	muscle
24	chr18:12595400-12598200	Enhancers	Brain Anterior Caudate	brain
25	chr18:12595400-12599400	Enhancers	Fetal Heart	heart
26	chr18:12595400-12600400	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr18:12595600-12596200	Enhancers	Primary hematopoietic stem cells	blood
28	chr18:12595600-12596200	Enhancers	Hela-S3	cervix
29	chr18:12595600-12596800	Enhancers	Primary T cells from cord blood	blood
30	chr18:12595600-12597200	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr18:12595600-12597200	Enhancers	HSMM	muscle
32	chr18:12595600-12597600	Enhancers	HUVEC	blood vessel
33	chr18:12595600-12598000	Enhancers	Brain Substantia Nigra	brain
34	chr18:12595600-12600400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr18:12595600-12600400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr18:12595600-12600600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr18:12595800-12596200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr18:12595800-12596200	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr18:12595800-12596400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr18:12595800-12596400	Enhancers	Brain Hippocampus Middle	brain
41	chr18:12595800-12596400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr18:12595800-12596600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr18:12595800-12598200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr18:12595800-12599000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr18:12595800-12600600	Enhancers	HMEC	breast
46	chr18:12596000-12596200	Enhancers	A549	lung
47	chr18:12596000-12597000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr18:12596000-12597000	Enhancers	K562	blood
49	chr18:12596000-12597400	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr18:12596000-12597600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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