Variant report

Variant	rs6134909
Chromosome Location	chr20:13537873-13537874
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	chr20:13526812..13528359-chr20:13536217..13539188,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11698396	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12329562	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13041649	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1973948	0.84[ASN][1000 genomes]
rs2073323	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2327789	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28444692	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2876356	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3789343	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3789344	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3789345	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3789350	0.91[EUR][1000 genomes]
rs4411781	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6033720	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6033723	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6033727	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6033731	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6033733	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6033735	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6033736	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6033737	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6033741	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6033745	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6033755	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042156	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6042167	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6042174	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6042176	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6042179	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6042181	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6042183	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6042184	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6042186	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6042212	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6042222	0.91[ASN][1000 genomes]
rs6105115	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6105116	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6109906	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6109908	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6109913	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6109915	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6131478	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6131480	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6131481	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6131482	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6134882	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6134883	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6134885	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6134890	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6134892	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6134893	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6134894	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6134896	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6134897	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6134899	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6134904	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6134907	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6134908	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6134911	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134913	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134914	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6134915	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6134918	0.91[ASN][1000 genomes]
rs73080067	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73086022	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73086039	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8115098	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8123095	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8124555	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8126063	0.83[ASN][1000 genomes]
rs8184309	0.90[AFR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6134909	TASP1	cis	lung	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

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	chr20:13503000-13538200	Weak transcription	Ovary	ovary
5	chr20:13506400-13558800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr20:13508000-13542000	Weak transcription	Fetal Intestine Small	intestine
7	chr20:13508000-13563600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr20:13508200-13556400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr20:13508400-13538000	Weak transcription	HepG2	liver
10	chr20:13508400-13546600	Weak transcription	Fetal Kidney	kidney
11	chr20:13508400-13550400	Weak transcription	GM12878-XiMat	blood
12	chr20:13508400-13556000	Weak transcription	HSMM	muscle
13	chr20:13508400-13559600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr20:13508400-13563400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr20:13509200-13548200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr20:13509200-13556000	Weak transcription	Fetal Stomach	stomach
17	chr20:13509800-13538600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr20:13509800-13547400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr20:13512800-13548400	Weak transcription	Left Ventricle	heart
20	chr20:13512800-13556000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr20:13513800-13547600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr20:13514800-13541000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr20:13514800-13546400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr20:13515000-13605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr20:13516600-13538200	Weak transcription	Thymus	Thymus
26	chr20:13526800-13561800	Weak transcription	Stomach Mucosa	stomach
27	chr20:13526800-13613800	Weak transcription	Hela-S3	cervix
28	chr20:13527000-13556000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr20:13527200-13540000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr20:13527400-13539000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr20:13527400-13552200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr20:13527400-13560000	Weak transcription	HSMMtube	muscle
33	chr20:13527400-13562200	Weak transcription	Aorta	Aorta
34	chr20:13527400-13563400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr20:13527600-13538200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr20:13527600-13559600	Weak transcription	HMEC	breast
37	chr20:13527800-13563400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr20:13529200-13539600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr20:13529200-13552200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr20:13529400-13555800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr20:13530600-13538000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr20:13530600-13547600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr20:13532200-13538400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr20:13532400-13547800	Weak transcription	Fetal Lung	lung
45	chr20:13532600-13541400	Weak transcription	Adipose Nuclei	Adipose
46	chr20:13532800-13538000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr20:13533400-13547000	Weak transcription	A549	lung
48	chr20:13534400-13540000	Weak transcription	Fetal Brain Male	brain
49	chr20:13534600-13563600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr20:13534600-13563600	Weak transcription	Lung	lung

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