Variant report

Variant	rs6134912
Chromosome Location	chr20:13545413-13545414
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13543205..13545985-chr20:13547825..13549640,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs13039162	0.86[ASN][1000 genomes]
rs13042843	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2057258	0.87[ASN][1000 genomes]
rs2070305	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2070334	0.81[ASN][1000 genomes]
rs2073324	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2103972	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2182708	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2208207	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2208208	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2273480	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3747931	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3789342	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3789347	0.83[ASN][1000 genomes]
rs3789348	0.83[ASN][1000 genomes]
rs3789349	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4813131	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4814236	0.88[ASN][1000 genomes]
rs4814238	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4814242	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57218913	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6042106	0.81[ASN][1000 genomes]
rs6042128	0.87[ASN][1000 genomes]
rs6042153	0.86[ASN][1000 genomes]
rs6074611	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6074612	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6074613	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6074618	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6074627	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079066	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6079072	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6079074	0.86[ASN][1000 genomes]
rs6079075	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6079077	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079085	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6079095	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079106	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6105096	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6105098	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6105103	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6105113	0.86[ASN][1000 genomes]
rs6109887	0.84[ASN][1000 genomes]
rs6109891	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6109903	0.83[ASN][1000 genomes]
rs6109905	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6109958	0.90[ASN][1000 genomes]
rs6131483	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6131485	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6131488	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6134879	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6134902	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73086013	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv585435	chr20:13410638-13582476	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv458871	chr20:13447896-13573415	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv585436	chr20:13447896-13573415	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv912687	chr20:13507057-13591596	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1797514	chr20:13541011-13610424	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13492200-13567000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr20:13497800-13563400	Weak transcription	Pancreas	Pancrea
3	chr20:13506400-13558800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr20:13508000-13563600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr20:13508200-13556400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr20:13508400-13546600	Weak transcription	Fetal Kidney	kidney
7	chr20:13508400-13550400	Weak transcription	GM12878-XiMat	blood
8	chr20:13508400-13556000	Weak transcription	HSMM	muscle
9	chr20:13508400-13559600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr20:13508400-13563400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr20:13509200-13548200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr20:13509200-13556000	Weak transcription	Fetal Stomach	stomach
13	chr20:13509800-13547400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr20:13512800-13548400	Weak transcription	Left Ventricle	heart
15	chr20:13512800-13556000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr20:13513800-13547600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr20:13514800-13546400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr20:13515000-13605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr20:13526800-13561800	Weak transcription	Stomach Mucosa	stomach
20	chr20:13526800-13613800	Weak transcription	Hela-S3	cervix
21	chr20:13527000-13556000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr20:13527400-13552200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr20:13527400-13560000	Weak transcription	HSMMtube	muscle
24	chr20:13527400-13562200	Weak transcription	Aorta	Aorta
25	chr20:13527400-13563400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr20:13527600-13559600	Weak transcription	HMEC	breast
27	chr20:13527800-13563400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr20:13529200-13552200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr20:13529400-13555800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr20:13530600-13547600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr20:13532400-13547800	Weak transcription	Fetal Lung	lung
32	chr20:13533400-13547000	Weak transcription	A549	lung
33	chr20:13534600-13563600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr20:13534600-13563600	Weak transcription	Lung	lung
35	chr20:13534800-13552200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr20:13535000-13559600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr20:13535000-13563400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr20:13535200-13560200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr20:13535400-13547400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr20:13535400-13556400	Weak transcription	Liver	Liver
41	chr20:13535600-13608000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr20:13535800-13547600	Weak transcription	Brain Angular Gyrus	brain
43	chr20:13535800-13552400	Weak transcription	NHDF-Ad	bronchial
44	chr20:13535800-13561400	Weak transcription	NHEK	skin
45	chr20:13536600-13551400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr20:13536600-13556000	Weak transcription	Fetal Muscle Leg	muscle
47	chr20:13536800-13563400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr20:13537400-13563600	Weak transcription	Placenta	Placenta
49	chr20:13537600-13556000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr20:13538200-13571800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links