Variant report

Variant	rs6134892
Chromosome Location	chr20:13481654-13481655
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11698396	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12329562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13041649	0.83[ASN][1000 genomes]
rs1973948	0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2073323	0.91[ASN][1000 genomes]
rs2327789	0.94[ASN][1000 genomes]
rs28444692	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2876356	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs3789343	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789344	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789345	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3789350	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4411781	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs6033720	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033723	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033727	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6033731	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033733	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6033735	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6033736	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033737	0.96[ASN][1000 genomes]
rs6033741	0.95[ASN][1000 genomes]
rs6033745	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs6033755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6042156	0.94[ASN][1000 genomes]
rs6042167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042174	0.96[ASN][1000 genomes]
rs6042176	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042179	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042181	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042183	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs6042184	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042186	0.95[ASN][1000 genomes]
rs6042212	0.82[ASN][1000 genomes]
rs6042222	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs6105115	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6105116	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6109906	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6109908	0.94[ASN][1000 genomes]
rs6109913	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6109915	0.95[ASN][1000 genomes]
rs6131478	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6131480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6131481	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6131482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6134872	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6134882	0.92[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs6134883	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs6134885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6134890	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6134893	0.93[ASN][1000 genomes]
rs6134894	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6134896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6134897	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6134899	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6134904	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6134907	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6134908	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6134909	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6134911	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6134913	1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6134914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6134915	0.83[ASN][1000 genomes]
rs6134918	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs6134928	0.81[MEX][hapmap]
rs6514391	0.83[EUR][1000 genomes]
rs7273818	0.81[MEX][hapmap]
rs73080067	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73080080	0.93[ASN][1000 genomes]
rs73086022	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8115098	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs8123095	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8124555	0.81[ASN][1000 genomes]
rs8126063	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8184309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6134892	TASP1	cis	cerebellum	SCAN
rs6134892	TASP1	cis	lung	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13463800-13505400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr20:13464000-13493800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr20:13464200-13483400	Weak transcription	Fetal Thymus	thymus
4	chr20:13468000-13483600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr20:13468200-13483600	Weak transcription	Right Ventricle	heart
6	chr20:13470200-13505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr20:13471800-13483400	Weak transcription	Fetal Intestine Small	intestine
8	chr20:13473400-13505800	Weak transcription	HSMM	muscle
9	chr20:13474000-13482000	Weak transcription	HMEC	breast
10	chr20:13474200-13482600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr20:13474400-13483000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr20:13474400-13483600	Weak transcription	Left Ventricle	heart
13	chr20:13474400-13496800	Weak transcription	Pancreas	Pancrea
14	chr20:13477400-13484000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr20:13478200-13503800	Weak transcription	Gastric	stomach
16	chr20:13479000-13482000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr20:13479000-13483400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr20:13479200-13486200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr20:13479400-13481800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
20	chr20:13479400-13483400	Weak transcription	Aorta	Aorta
21	chr20:13479600-13483400	Weak transcription	Fetal Stomach	stomach
22	chr20:13480000-13482200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
23	chr20:13480000-13482400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr20:13480000-13488200	Weak transcription	NHEK	skin
25	chr20:13480000-13490400	ZNF genes & repeats	Dnd41	blood
26	chr20:13480200-13483400	Weak transcription	Ovary	ovary
27	chr20:13480200-13484400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr20:13480400-13483400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr20:13480400-13483400	Weak transcription	Thymus	Thymus
30	chr20:13480800-13483200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr20:13480800-13483400	Weak transcription	Primary B cells from cord blood	blood
32	chr20:13481200-13481800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
33	chr20:13481200-13482200	ZNF genes & repeats	Liver	Liver
34	chr20:13481400-13481800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
35	chr20:13481400-13483400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr20:13481600-13482400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links