Variant report

Variant	rs2070334
Chromosome Location	chr20:13433707-13433708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs13039162	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13042843	0.94[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1474954	0.83[YRI][hapmap]
rs2057258	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs2057259	0.89[LWK][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap]
rs2070305	0.94[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2073324	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2182708	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2208207	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2208208	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2273477	0.86[YRI][hapmap]
rs2273480	1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2295504	0.80[ASW][hapmap]
rs3747931	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789342	0.94[CHB][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3789347	0.92[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789348	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789349	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3827703	0.86[YRI][hapmap]
rs4813131	0.94[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4814234	0.83[YRI][hapmap]
rs4814236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4814238	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4814242	0.94[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs57218913	0.84[ASN][1000 genomes]
rs6033705	0.89[YRI][hapmap]
rs6042106	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6042128	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042153	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6042262	0.80[LWK][hapmap]
rs6074611	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6074612	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6074613	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6074618	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6074627	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs6079066	0.94[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6079072	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6079074	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6079075	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6079077	1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6079085	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6079095	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]
rs6079106	0.94[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs6105096	0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs6105098	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6105103	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6105113	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6109887	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6109891	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6109903	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6109905	0.94[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6109958	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs6109983	0.80[ASW][hapmap]
rs6131483	0.94[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6131485	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6131488	0.94[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs6134879	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6134902	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6134912	0.81[ASN][1000 genomes]
rs6134919	0.89[LWK][hapmap];0.94[MKK][hapmap];0.82[YRI][hapmap]
rs73086013	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs932568	0.83[YRI][hapmap]

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	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	esv21228	chr20:13283535-13447810	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	nsv520595	chr20:13421045-13447896	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2070334	TASP1	cis	multi-tissue	Pritchard

Chromatin state (count:46 , 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	chr20:13403800-13435000	Weak transcription	HMEC	breast
4	chr20:13404400-13434800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr20:13404400-13434800	Weak transcription	NHEK	skin
6	chr20:13411400-13435000	Weak transcription	Lung	lung
7	chr20:13415400-13435000	Weak transcription	Placenta	Placenta
8	chr20:13416000-13438200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr20:13416200-13435000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr20:13416200-13436600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr20:13416400-13434600	Weak transcription	Fetal Thymus	thymus
12	chr20:13420800-13444400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr20:13421800-13436600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr20:13421800-13450000	Weak transcription	Fetal Lung	lung
15	chr20:13422000-13460400	Weak transcription	Primary B cells from cord blood	blood
16	chr20:13422000-13461200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr20:13422200-13435000	Weak transcription	Aorta	Aorta
18	chr20:13422400-13435200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr20:13423200-13433800	Weak transcription	K562	blood
20	chr20:13424600-13435000	Weak transcription	Fetal Muscle Leg	muscle
21	chr20:13428200-13434600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr20:13428400-13433800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr20:13428400-13448800	Weak transcription	Thymus	Thymus
24	chr20:13429800-13437000	Strong transcription	Dnd41	blood
25	chr20:13430000-13467800	Weak transcription	Ovary	ovary
26	chr20:13430200-13433800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr20:13430200-13467800	Weak transcription	Pancreas	Pancrea
28	chr20:13430400-13442200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr20:13430600-13435400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr20:13430600-13436000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr20:13431400-13436000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr20:13431600-13435200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr20:13431600-13445000	Weak transcription	Adipose Nuclei	Adipose
34	chr20:13431800-13435000	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr20:13432000-13435400	Strong transcription	Primary T cells from cord blood	blood
36	chr20:13432200-13438400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr20:13432400-13448800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr20:13432600-13435200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr20:13432600-13437400	Enhancers	Liver	Liver
40	chr20:13432800-13434400	Enhancers	HepG2	liver
41	chr20:13433400-13434000	Strong transcription	Primary hematopoietic stem cells	blood
42	chr20:13433400-13435600	Strong transcription	Primary B cells from peripheral blood	blood
43	chr20:13433600-13433800	Enhancers	Small Intestine	intestine
44	chr20:13433600-13434000	Enhancers	Fetal Intestine Large	intestine
45	chr20:13433600-13434400	Enhancers	A549	lung
46	chr20:13433600-13434800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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