Variant report

Variant	rs6134872
Chromosome Location	chr20:13418535-13418536
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	chr20:13408378..13410884-chr20:13417652..13421238,3	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs12329562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2073323	0.83[ASN][1000 genomes]
rs2327789	0.85[ASN][1000 genomes]
rs2876356	0.86[ASN][1000 genomes]
rs3789343	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3789344	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3789345	0.86[ASN][1000 genomes]
rs3789350	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4411781	0.86[ASN][1000 genomes]
rs6033720	0.85[ASN][1000 genomes]
rs6033723	0.85[ASN][1000 genomes]
rs6033727	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6033731	0.86[ASN][1000 genomes]
rs6033733	0.85[ASN][1000 genomes]
rs6033735	0.85[ASN][1000 genomes]
rs6033736	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6033737	0.85[ASN][1000 genomes]
rs6033741	0.86[ASN][1000 genomes]
rs6033745	0.83[ASN][1000 genomes]
rs6042156	0.85[ASN][1000 genomes]
rs6042167	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6042174	0.85[ASN][1000 genomes]
rs6042176	0.85[ASN][1000 genomes]
rs6042179	0.85[ASN][1000 genomes]
rs6042181	0.85[ASN][1000 genomes]
rs6042183	0.86[ASN][1000 genomes]
rs6042184	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6042186	0.86[ASN][1000 genomes]
rs6105115	0.85[ASN][1000 genomes]
rs6105116	0.86[ASN][1000 genomes]
rs6109906	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6109908	0.85[ASN][1000 genomes]
rs6109913	0.85[ASN][1000 genomes]
rs6109915	0.86[ASN][1000 genomes]
rs6131478	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6131480	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6131481	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6131482	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6134882	0.86[ASN][1000 genomes]
rs6134883	0.86[ASN][1000 genomes]
rs6134885	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6134890	0.85[ASN][1000 genomes]
rs6134892	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6134893	0.85[ASN][1000 genomes]
rs6134894	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6134896	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6134897	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6134899	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6134904	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6134907	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6134908	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6134911	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6134918	0.85[EUR][1000 genomes]
rs6514391	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73080067	0.86[ASN][1000 genomes]
rs73080080	0.85[ASN][1000 genomes]
rs73086022	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8115098	0.86[ASN][1000 genomes]
rs8126063	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6134872	TASP1	cis	lung	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13379200-13463000	Weak transcription	HSMM	muscle
2	chr20:13392600-13421400	Weak transcription	Psoas Muscle	Psoas
3	chr20:13395600-13477800	Weak transcription	Gastric	stomach
4	chr20:13397400-13421200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr20:13399800-13430800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr20:13403800-13435000	Weak transcription	HMEC	breast
7	chr20:13404400-13434800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr20:13404400-13434800	Weak transcription	NHEK	skin
9	chr20:13408000-13419600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr20:13409000-13419600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr20:13410000-13421600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr20:13411400-13435000	Weak transcription	Lung	lung
13	chr20:13411600-13421400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr20:13412600-13421800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr20:13412600-13424200	Weak transcription	HepG2	liver
16	chr20:13412800-13420600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr20:13413600-13433400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr20:13415200-13428000	Weak transcription	Thymus	Thymus
19	chr20:13415400-13419000	Weak transcription	Fetal Muscle Leg	muscle
20	chr20:13415400-13419400	Weak transcription	Fetal Lung	lung
21	chr20:13415400-13420400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr20:13415400-13420600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr20:13415400-13435000	Weak transcription	Placenta	Placenta
24	chr20:13415600-13418600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr20:13415600-13433600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr20:13415800-13419200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr20:13415800-13419600	Weak transcription	Ovary	ovary
28	chr20:13416000-13419000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr20:13416000-13438200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr20:13416200-13420800	Weak transcription	Primary B cells from cord blood	blood
31	chr20:13416200-13421000	Weak transcription	Primary T cells from cord blood	blood
32	chr20:13416200-13435000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr20:13416200-13436600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr20:13416400-13434600	Weak transcription	Fetal Thymus	thymus
35	chr20:13417400-13423600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr20:13417600-13420600	Weak transcription	Dnd41	blood

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