Variant report

Variant	rs6109903
Chromosome Location	chr20:13452638-13452639
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs13039162	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13042843	0.84[ASN][1000 genomes]
rs2057258	0.81[EUR][1000 genomes]
rs2070305	0.85[ASN][1000 genomes]
rs2070334	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2073324	0.86[ASN][1000 genomes]
rs2103972	0.80[ASN][1000 genomes]
rs2182708	0.88[ASN][1000 genomes]
rs2208207	0.83[ASN][1000 genomes]
rs2208208	0.88[ASN][1000 genomes]
rs2273480	0.90[ASN][1000 genomes]
rs3747931	0.82[ASN][1000 genomes]
rs3789342	0.89[ASN][1000 genomes]
rs3789347	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3789348	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3789349	0.87[ASN][1000 genomes]
rs4813131	0.88[ASN][1000 genomes]
rs4814236	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4814238	0.88[ASN][1000 genomes]
rs4814242	0.82[ASN][1000 genomes]
rs57218913	0.92[ASN][1000 genomes]
rs6042106	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6042128	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6042153	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6074611	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6074612	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6074613	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6074618	0.88[ASN][1000 genomes]
rs6079066	0.88[ASN][1000 genomes]
rs6079072	0.83[ASN][1000 genomes]
rs6079074	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6079075	0.84[ASN][1000 genomes]
rs6079077	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6079085	0.86[ASN][1000 genomes]
rs6079095	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6079106	0.84[ASN][1000 genomes]
rs6105096	0.88[ASN][1000 genomes]
rs6105098	0.88[ASN][1000 genomes]
rs6105103	0.81[ASN][1000 genomes]
rs6105113	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6109887	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6109891	0.89[ASN][1000 genomes]
rs6109905	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6131483	0.87[ASN][1000 genomes]
rs6131485	0.88[ASN][1000 genomes]
rs6131488	0.82[ASN][1000 genomes]
rs6134879	0.90[ASN][1000 genomes]
rs6134902	0.87[ASN][1000 genomes]
rs6134912	0.83[ASN][1000 genomes]
rs73086013	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3425983	chr20:13046768-13461834	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1062049	chr20:13347580-13477455	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv544186	chr20:13347580-13477455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13379200-13463000	Weak transcription	HSMM	muscle
2	chr20:13395600-13477800	Weak transcription	Gastric	stomach
3	chr20:13422000-13460400	Weak transcription	Primary B cells from cord blood	blood
4	chr20:13422000-13461200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr20:13430000-13467800	Weak transcription	Ovary	ovary
6	chr20:13430200-13467800	Weak transcription	Pancreas	Pancrea
7	chr20:13435400-13460400	Weak transcription	Fetal Thymus	thymus
8	chr20:13435400-13462000	Weak transcription	Left Ventricle	heart
9	chr20:13435600-13454200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr20:13435600-13460600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr20:13436600-13458800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr20:13436600-13460800	Weak transcription	Primary T cells from cord blood	blood
13	chr20:13442600-13461800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr20:13442600-13471600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr20:13442800-13467800	Weak transcription	Aorta	Aorta
16	chr20:13443400-13461200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr20:13445000-13460200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr20:13445400-13467800	Weak transcription	Fetal Stomach	stomach
19	chr20:13445600-13461000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr20:13446200-13460800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr20:13450200-13460400	Weak transcription	Fetal Lung	lung
22	chr20:13450200-13461000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr20:13450200-13461800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr20:13450400-13457600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr20:13450400-13461000	Weak transcription	HepG2	liver
26	chr20:13450400-13461200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr20:13450800-13461200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr20:13451600-13464200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr20:13452000-13458400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr20:13452000-13458600	Weak transcription	Fetal Brain Male	brain
31	chr20:13452600-13454200	Weak transcription	Dnd41	blood
32	chr20:13452600-13454400	Weak transcription	Fetal Intestine Small	intestine
33	chr20:13452600-13460400	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links