Variant report

Variant	rs6079095
Chromosome Location	chr20:13520928-13520929
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs13039162	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13042843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2057258	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs2057259	0.81[JPT][hapmap]
rs2070305	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2070334	0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2073324	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2103972	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2180569	0.81[JPT][hapmap]
rs2182708	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2208207	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2208208	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2273480	0.92[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3747931	0.91[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3789342	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3789347	0.94[CHB][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3789348	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3789349	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4813131	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4814236	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4814238	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4814242	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57218913	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6042106	0.94[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6042128	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6042153	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6074611	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6074612	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6074613	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6074618	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6074627	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6079058	0.82[CHD][hapmap]
rs6079066	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6079072	0.92[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6079074	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079075	0.92[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6079077	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6079085	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079106	1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.94[ASN][1000 genomes]
rs6105096	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6105098	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6105103	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6105113	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6109887	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6109891	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6109903	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6109905	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6109958	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6131476	0.82[CHD][hapmap]
rs6131483	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6131485	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6131488	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6134879	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6134902	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6134912	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6134919	0.81[JPT][hapmap]
rs73086013	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6079095	TASP1	cis	cerebellum	SCAN
rs6079095	TASP1	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13485000-13543600	Weak transcription	Small Intestine	intestine
2	chr20:13492200-13567000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr20:13497800-13563400	Weak transcription	Pancreas	Pancrea
4	chr20:13503000-13537600	Weak transcription	Psoas Muscle	Psoas
5	chr20:13503000-13538200	Weak transcription	Ovary	ovary
6	chr20:13504200-13527000	Strong transcription	Dnd41	blood
7	chr20:13506400-13558800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr20:13507800-13526200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr20:13508000-13527000	Weak transcription	NHEK	skin
10	chr20:13508000-13534000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr20:13508000-13542000	Weak transcription	Fetal Intestine Small	intestine
12	chr20:13508000-13563600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr20:13508200-13525000	Weak transcription	A549	lung
14	chr20:13508200-13556400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr20:13508400-13538000	Weak transcription	HepG2	liver
16	chr20:13508400-13546600	Weak transcription	Fetal Kidney	kidney
17	chr20:13508400-13550400	Weak transcription	GM12878-XiMat	blood
18	chr20:13508400-13556000	Weak transcription	HSMM	muscle
19	chr20:13508400-13559600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr20:13508400-13563400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr20:13509000-13527200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr20:13509000-13528000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr20:13509200-13536200	Weak transcription	Fetal Intestine Large	intestine
24	chr20:13509200-13548200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr20:13509200-13556000	Weak transcription	Fetal Stomach	stomach
26	chr20:13509600-13527200	Weak transcription	Liver	Liver
27	chr20:13509800-13526600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr20:13509800-13536200	Weak transcription	Fetal Muscle Leg	muscle
29	chr20:13509800-13538600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr20:13509800-13547400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr20:13512800-13548400	Weak transcription	Left Ventricle	heart
32	chr20:13512800-13556000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr20:13513000-13526800	Weak transcription	Aorta	Aorta
34	chr20:13513800-13547600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr20:13514000-13532000	Weak transcription	Primary B cells from cord blood	blood
36	chr20:13514000-13536200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr20:13514400-13526200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr20:13514400-13527000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr20:13514800-13536600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr20:13514800-13541000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr20:13514800-13546400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr20:13515000-13605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr20:13516400-13529000	Weak transcription	Fetal Thymus	thymus
44	chr20:13516600-13528600	Weak transcription	Primary T cells from cord blood	blood
45	chr20:13516600-13538200	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links