Variant report

Variant	rs3789345
Chromosome Location	chr20:13471848-13471849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13442182..13443887-chr20:13469924..13472728,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs11698396	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs11698691	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12329562	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13041649	0.80[ASN][1000 genomes]
rs1973948	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs2073323	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2327789	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28444692	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2876356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789343	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789344	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789350	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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033720	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6033723	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6033727	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033733	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6033735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6033736	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033737	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6033741	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033745	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6033755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6042156	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042174	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042176	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042179	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042183	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042184	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042186	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042212	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6042222	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap]
rs6105115	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6105116	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109906	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6109908	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6109913	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6109915	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6131478	0.95[ASN][1000 genomes]
rs6131480	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6131481	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6131482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6134872	0.86[ASN][1000 genomes]
rs6134882	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134883	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6134890	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6134892	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6134893	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6134894	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6134896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6134897	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6134899	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6134904	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6134907	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs6134908	0.85[ASN][1000 genomes]
rs6134909	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6134911	0.80[ASN][1000 genomes]
rs6134913	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6134914	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs6134915	0.80[ASN][1000 genomes]
rs6134918	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs73080067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73080080	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73086022	0.80[ASN][1000 genomes]
rs73086039	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8115098	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8123095	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8124555	0.81[EUR][1000 genomes]
rs8126063	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs8184309	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[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
rs3789345	TASP1	cis	lung	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13395600-13477800	Weak transcription	Gastric	stomach
2	chr20:13458600-13472600	Weak transcription	Psoas Muscle	Psoas
3	chr20:13459400-13472000	Weak transcription	HSMMtube	muscle
4	chr20:13459600-13472600	Weak transcription	NH-A	brain
5	chr20:13460600-13472600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr20:13460800-13472000	Weak transcription	Brain Hippocampus Middle	brain
7	chr20:13460800-13472000	Weak transcription	NHEK	skin
8	chr20:13461400-13472000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr20:13461800-13472000	Weak transcription	NHDF-Ad	bronchial
10	chr20:13462200-13477800	Weak transcription	Thymus	Thymus
11	chr20:13463400-13480200	Weak transcription	Brain Angular Gyrus	brain
12	chr20:13463800-13472000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr20:13463800-13481200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr20:13463800-13505400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr20:13464000-13472000	Weak transcription	Adipose Nuclei	Adipose
16	chr20:13464000-13472400	Weak transcription	A549	lung
17	chr20:13464000-13473800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr20:13464000-13473800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr20:13464000-13474800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr20:13464000-13475200	Weak transcription	Fetal Kidney	kidney
21	chr20:13464000-13479000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr20:13464000-13493800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr20:13464200-13472000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr20:13464200-13472000	Weak transcription	HMEC	breast
25	chr20:13464200-13472600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr20:13464200-13472600	Weak transcription	Left Ventricle	heart
27	chr20:13464200-13472800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr20:13464200-13473000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr20:13464200-13475800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr20:13464200-13477800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr20:13464200-13478000	Weak transcription	Primary B cells from peripheral blood	blood
32	chr20:13464200-13479200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr20:13464200-13480200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr20:13464200-13483400	Weak transcription	Fetal Thymus	thymus
35	chr20:13464400-13474800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr20:13464400-13479400	Weak transcription	Primary B cells from cord blood	blood
37	chr20:13465400-13480000	Strong transcription	Dnd41	blood
38	chr20:13467800-13477800	Weak transcription	Primary T cells from cord blood	blood
39	chr20:13468000-13472600	Weak transcription	Ovary	ovary
40	chr20:13468000-13483600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr20:13468200-13472400	Weak transcription	HSMM	muscle
42	chr20:13468200-13472600	Weak transcription	Fetal Lung	lung
43	chr20:13468200-13472600	Weak transcription	Fetal Stomach	stomach
44	chr20:13468200-13473800	Weak transcription	Pancreas	Pancrea
45	chr20:13468200-13477800	Weak transcription	Aorta	Aorta
46	chr20:13468200-13481200	Weak transcription	Liver	Liver
47	chr20:13468200-13483600	Weak transcription	Right Ventricle	heart
48	chr20:13468400-13472200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr20:13468400-13472800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr20:13469400-13472400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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