Variant report

Variant	rs6109906
Chromosome Location	chr20:13462515-13462516
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11698396	0.85[ASN][1000 genomes]
rs12329562	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13041649	0.85[ASN][1000 genomes]
rs2073323	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2327789	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28444692	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2876356	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3789343	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789344	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789345	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3789350	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4411781	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033720	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6033723	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6033727	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033731	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033733	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033735	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033736	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6033737	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033741	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033745	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033755	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6042156	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042167	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042174	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042176	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042179	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042181	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042183	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6042184	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042186	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6042212	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6105115	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6105116	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6109908	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6109913	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6109915	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6131478	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6131480	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6131481	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6131482	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6134872	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6134882	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6134883	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6134885	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6134890	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6134892	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6134893	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6134894	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6134896	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6134897	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6134899	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134904	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6134907	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6134908	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6134909	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6134911	0.85[ASN][1000 genomes]
rs6134913	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6134914	0.85[ASN][1000 genomes]
rs6134915	0.85[ASN][1000 genomes]
rs73080067	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73080080	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73086022	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73086039	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8115098	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8123095	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8124555	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8126063	0.98[ASN][1000 genomes]
rs8184309	0.85[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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6109906	TASP1	cis	lung	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

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	chr20:13430000-13467800	Weak transcription	Ovary	ovary
4	chr20:13430200-13467800	Weak transcription	Pancreas	Pancrea
5	chr20:13442600-13471600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr20:13442800-13467800	Weak transcription	Aorta	Aorta
7	chr20:13445400-13467800	Weak transcription	Fetal Stomach	stomach
8	chr20:13451600-13464200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr20:13454400-13471200	Weak transcription	Small Intestine	intestine
10	chr20:13455400-13463800	Strong transcription	Dnd41	blood
11	chr20:13457000-13471400	Weak transcription	Hela-S3	cervix
12	chr20:13457800-13462600	Weak transcription	Brain Angular Gyrus	brain
13	chr20:13457800-13466000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr20:13458000-13470600	Weak transcription	Colon Smooth Muscle	Colon
15	chr20:13458000-13471600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr20:13458600-13472600	Weak transcription	Psoas Muscle	Psoas
17	chr20:13458800-13463200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr20:13458800-13464200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr20:13459400-13472000	Weak transcription	HSMMtube	muscle
20	chr20:13459600-13462600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr20:13459600-13469800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr20:13459600-13472600	Weak transcription	NH-A	brain
23	chr20:13459800-13465800	Weak transcription	Spleen	Spleen
24	chr20:13460200-13462600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr20:13460200-13462600	Weak transcription	Placenta	Placenta
26	chr20:13460200-13463600	Weak transcription	GM12878-XiMat	blood
27	chr20:13460200-13464000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr20:13460200-13471600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr20:13460400-13464000	Strong transcription	Liver	Liver
30	chr20:13460400-13464000	Strong transcription	Fetal Lung	lung
31	chr20:13460400-13464200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr20:13460400-13464200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr20:13460400-13464200	Strong transcription	Fetal Thymus	thymus
34	chr20:13460600-13464200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr20:13460600-13464200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr20:13460600-13469800	Weak transcription	Fetal Brain Female	brain
37	chr20:13460600-13472600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr20:13460800-13462600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr20:13460800-13463400	Strong transcription	Primary T cells from cord blood	blood
40	chr20:13460800-13463600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr20:13460800-13464000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr20:13460800-13464200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr20:13460800-13464200	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr20:13460800-13464200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr20:13460800-13472000	Weak transcription	Brain Hippocampus Middle	brain
46	chr20:13460800-13472000	Weak transcription	NHEK	skin
47	chr20:13461000-13462600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr20:13461000-13463800	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr20:13461000-13463800	Strong transcription	HepG2	liver
50	chr20:13461000-13464000	Strong transcription	Primary T cells fromperipheralblood	blood

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