Variant report

Variant	rs3789350
Chromosome Location	chr20:13416552-13416553
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11698396	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11698691	0.81[EUR][1000 genomes]
rs12329562	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs1973948	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs2073323	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2327789	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28444692	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2876356	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789343	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3789344	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3789345	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4411781	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6033720	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033723	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033727	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6033731	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6033733	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033735	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033736	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6033737	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033741	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6033745	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6033755	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6042156	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6042167	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042174	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6042176	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6042179	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6042181	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6042183	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042184	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042186	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042212	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6042222	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap]
rs6105115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6105116	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6109906	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6109908	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6109913	0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6109915	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6131478	0.93[ASN][1000 genomes]
rs6131480	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs6131481	0.93[ASN][1000 genomes]
rs6131482	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6134872	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6134882	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6134883	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6134885	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6134890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6134892	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs6134893	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6134894	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6134896	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6134897	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6134899	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6134904	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6134907	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs6134908	0.83[ASN][1000 genomes]
rs6134909	0.91[EUR][1000 genomes]
rs6134913	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs6134914	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6134918	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs73080067	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73080080	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73086039	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8115098	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8123095	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8124555	0.80[EUR][1000 genomes]
rs8126063	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs8184309	1.00[CHB][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3789350	TASP1	cis	cerebellum	SCAN
rs3789350	TASP1	cis	parietal	SCAN
rs3789350	TASP1	cis	lung	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13364600-13416800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr20:13374200-13417200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr20:13379200-13463000	Weak transcription	HSMM	muscle
4	chr20:13392600-13421400	Weak transcription	Psoas Muscle	Psoas
5	chr20:13393800-13416800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr20:13394200-13416800	Weak transcription	Esophagus	oesophagus
7	chr20:13394200-13417200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr20:13395600-13416800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr20:13395600-13477800	Weak transcription	Gastric	stomach
10	chr20:13396000-13417000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr20:13397400-13421200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr20:13398200-13416800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr20:13398200-13417800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr20:13399800-13430800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr20:13403800-13435000	Weak transcription	HMEC	breast
16	chr20:13404400-13434800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr20:13404400-13434800	Weak transcription	NHEK	skin
18	chr20:13405400-13417200	Weak transcription	Small Intestine	intestine
19	chr20:13406800-13417400	Weak transcription	Colon Smooth Muscle	Colon
20	chr20:13407800-13417200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr20:13408000-13417400	Weak transcription	Fetal Brain Female	brain
22	chr20:13408000-13419600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr20:13408400-13417000	Weak transcription	Brain Anterior Caudate	brain
24	chr20:13408800-13416800	Weak transcription	Colonic Mucosa	Colon
25	chr20:13409000-13416800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr20:13409000-13419600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr20:13409200-13417400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr20:13410000-13421600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr20:13410600-13417400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr20:13411400-13417400	Weak transcription	Fetal Stomach	stomach
31	chr20:13411400-13435000	Weak transcription	Lung	lung
32	chr20:13411600-13416600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr20:13411600-13421400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr20:13412400-13417600	Strong transcription	Dnd41	blood
35	chr20:13412600-13421800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr20:13412600-13424200	Weak transcription	HepG2	liver
37	chr20:13412800-13420600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr20:13413200-13417800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr20:13413600-13417200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr20:13413600-13433400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr20:13414400-13416800	Weak transcription	Brain Germinal Matrix	brain
42	chr20:13414800-13417400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr20:13415000-13417400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr20:13415200-13417600	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr20:13415200-13428000	Weak transcription	Thymus	Thymus
46	chr20:13415400-13416600	Weak transcription	Aorta	Aorta
47	chr20:13415400-13416600	Weak transcription	Left Ventricle	heart
48	chr20:13415400-13416600	Weak transcription	Pancreas	Pancrea
49	chr20:13415400-13416800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr20:13415400-13417200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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