Variant report

Variant	rs28420983
Chromosome Location	chr14:71229486-71229487
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71221857..71224156-chr14:71229104..71232104,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10129495	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10131177	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10131364	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10141804	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10143748	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10147150	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10873243	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11158882	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11621281	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624934	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11625330	0.89[EUR][1000 genomes]
rs11628333	0.88[ASN][1000 genomes]
rs12886990	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12887479	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12888427	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12897648	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17108492	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1987652	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2158530	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2158531	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902843	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4902846	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902849	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66736782	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71425216	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71425219	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8008802	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8019261	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8019448	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8020663	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8022333	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8022401	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9323548	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71206800-71231600	Weak transcription	Brain Anterior Caudate	brain
2	chr14:71209400-71238200	Weak transcription	Fetal Stomach	stomach
3	chr14:71209400-71238400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:71209400-71238400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr14:71212000-71238200	Weak transcription	Fetal Intestine Small	intestine
6	chr14:71215800-71232200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr14:71216400-71238200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:71216600-71245800	Weak transcription	Brain Germinal Matrix	brain
9	chr14:71216800-71238400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr14:71220600-71231400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr14:71220600-71238600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr14:71220800-71240400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr14:71220800-71266400	Weak transcription	Fetal Intestine Large	intestine
14	chr14:71221000-71237600	Weak transcription	Fetal Kidney	kidney
15	chr14:71221800-71239600	Weak transcription	Liver	Liver
16	chr14:71222200-71238000	Weak transcription	Esophagus	oesophagus
17	chr14:71222200-71238200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr14:71222200-71238200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr14:71222200-71258200	Weak transcription	HepG2	liver
20	chr14:71222400-71230400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr14:71222400-71238200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr14:71222600-71274600	Weak transcription	Hela-S3	cervix
23	chr14:71222800-71238200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr14:71223000-71258400	Weak transcription	Primary T cells from cord blood	blood
25	chr14:71223000-71266600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:71223400-71240000	Weak transcription	Pancreas	Pancrea
27	chr14:71223600-71230600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr14:71223600-71232200	Weak transcription	Primary B cells from cord blood	blood
29	chr14:71224000-71258000	Weak transcription	Dnd41	blood
30	chr14:71227600-71238000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr14:71227800-71235200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr14:71227800-71238000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr14:71227800-71238400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr14:71227800-71245200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr14:71227800-71245600	Weak transcription	Lung	lung
36	chr14:71227800-71257800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr14:71228000-71229800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr14:71228000-71229800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr14:71228000-71235000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr14:71228000-71235200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr14:71228000-71236400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr14:71228000-71237800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr14:71228000-71238200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr14:71228000-71238200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr14:71228000-71238400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr14:71228000-71238400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr14:71228000-71242000	Weak transcription	GM12878-XiMat	blood
48	chr14:71228000-71245600	Weak transcription	Gastric	stomach
49	chr14:71228000-71258000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr14:71228000-71258000	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links