Variant report

Variant	rs6134899
Chromosome Location	chr20:13499446-13499447
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11698396	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12329562	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13041649	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2073323	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2327789	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28444692	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2876356	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3789343	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789345	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3789350	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4411781	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033720	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6033723	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6033727	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033731	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033733	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033735	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033736	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6033737	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033741	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6033745	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033755	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6042156	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042167	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042174	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042176	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042179	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042181	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042183	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6042184	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042186	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6042212	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6105115	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6105116	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6109906	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109908	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6109913	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6109915	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6131478	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6131480	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6131481	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6131482	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6134872	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6134882	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6134883	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6134885	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6134890	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6134892	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6134893	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6134894	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6134896	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6134897	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6134904	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6134907	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6134908	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6134909	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6134911	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6134913	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6134914	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6134915	0.85[ASN][1000 genomes]
rs73080067	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73080080	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73086022	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73086039	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8115098	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8123095	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8124555	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8126063	0.98[ASN][1000 genomes]
rs8184309	0.85[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6134899	TASP1	cis	lung	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13463800-13505400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr20:13470200-13505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr20:13473400-13505800	Weak transcription	HSMM	muscle
4	chr20:13478200-13503800	Weak transcription	Gastric	stomach
5	chr20:13483200-13509200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr20:13484000-13502600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr20:13484000-13502600	Weak transcription	Primary T cells from cord blood	blood
8	chr20:13484000-13502600	Weak transcription	Fetal Stomach	stomach
9	chr20:13485000-13502600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr20:13485000-13543600	Weak transcription	Small Intestine	intestine
11	chr20:13486200-13502600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr20:13487600-13515000	Weak transcription	Brain Germinal Matrix	brain
13	chr20:13488200-13502600	Weak transcription	Lung	lung
14	chr20:13488200-13502600	Weak transcription	Ovary	ovary
15	chr20:13489000-13502600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr20:13489000-13502600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr20:13489000-13502600	Weak transcription	Fetal Intestine Large	intestine
18	chr20:13489200-13514600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr20:13490400-13502800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr20:13490400-13509600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr20:13490800-13502800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr20:13491800-13503400	Weak transcription	Liver	Liver
23	chr20:13492200-13499600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr20:13492200-13503800	Weak transcription	Right Ventricle	heart
25	chr20:13492200-13505600	Weak transcription	Spleen	Spleen
26	chr20:13492200-13567000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr20:13492600-13502600	Weak transcription	Brain Hippocampus Middle	brain
28	chr20:13493600-13502800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr20:13493600-13505400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr20:13493600-13507600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr20:13493600-13510800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr20:13493600-13519200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr20:13493800-13504000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr20:13494000-13502600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr20:13494000-13502600	Weak transcription	A549	lung
36	chr20:13494000-13504000	Weak transcription	Fetal Intestine Small	intestine
37	chr20:13494000-13505400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr20:13494000-13507800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr20:13494000-13512400	Weak transcription	Placenta	Placenta
40	chr20:13494000-13515600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr20:13494200-13502800	Weak transcription	Fetal Muscle Leg	muscle
42	chr20:13494200-13516000	Weak transcription	Colonic Mucosa	Colon
43	chr20:13494400-13502600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr20:13494400-13506400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr20:13494400-13507600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr20:13494400-13507600	Weak transcription	GM12878-XiMat	blood
47	chr20:13494400-13514800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr20:13494600-13502600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr20:13494600-13503800	Weak transcription	Adipose Nuclei	Adipose
50	chr20:13494600-13516400	Weak transcription	Esophagus	oesophagus

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