Variant report

Variant	rs13136172
Chromosome Location	chr4:16218496-16218497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:16217489-16218963	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:16218115-16218514	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:16218406-16218778	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:16216932..16218804-chr4:16227245..16229857,2	MCF-7	breast:
2	chr4:16212529..16219737-chr4:16225844..16229602,8	MCF-7	breast:

Variant related genes	Relation type
TAPT1	TF binding region
ENSG00000169762	Chromatin interaction
ENSG00000263327	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10017532	0.81[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs10516297	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.92[ASN][1000 genomes]
rs11730922	0.92[ASN][1000 genomes]
rs13110290	0.84[ASN][1000 genomes]
rs13120908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13132678	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13136055	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2028631	0.83[ASN][1000 genomes]
rs28654954	0.80[ASN][1000 genomes]
rs2872216	0.93[ASN][1000 genomes]
rs33980476	0.90[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs34129131	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34496855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34592687	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34663238	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34837883	0.95[EUR][1000 genomes]
rs35475888	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35517826	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35804424	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35806798	0.96[ASN][1000 genomes]
rs35899968	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35931597	0.82[ASN][1000 genomes]
rs3749544	0.94[ASN][1000 genomes]
rs4235382	0.88[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs4481232	0.84[ASN][1000 genomes]
rs4571326	0.84[ASN][1000 genomes]
rs4698138	0.90[CHD][hapmap];0.83[JPT][hapmap]
rs4698457	0.81[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs56353092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810390	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6823229	0.92[ASN][1000 genomes]
rs6823230	0.92[ASN][1000 genomes]
rs6852432	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9995025	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh 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
rs13136172	TAPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16181200-16223800	Weak transcription	Fetal Brain Male	brain
2	chr4:16193000-16225800	Weak transcription	Colonic Mucosa	Colon
3	chr4:16193200-16225800	Weak transcription	Fetal Brain Female	brain
4	chr4:16198600-16221200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:16198600-16222400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:16198800-16218800	Weak transcription	HSMM	muscle
7	chr4:16198800-16225600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:16198800-16226000	Weak transcription	NHEK	skin
9	chr4:16198800-16226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:16202800-16220800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:16204800-16226600	Weak transcription	NH-A	brain
12	chr4:16205200-16225600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:16207400-16223600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:16208400-16219000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:16208400-16224400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr4:16208400-16225200	Weak transcription	Fetal Kidney	kidney
17	chr4:16208400-16225800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:16208800-16225600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:16208800-16225600	Weak transcription	Esophagus	oesophagus
20	chr4:16208800-16225600	Weak transcription	Gastric	stomach
21	chr4:16208800-16225800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:16208800-16225800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:16208800-16227200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:16209000-16225600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr4:16209200-16223400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:16209200-16225600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:16209200-16225600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:16209400-16226200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:16209400-16226200	Weak transcription	HSMMtube	muscle
30	chr4:16209600-16221400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:16210400-16225800	Weak transcription	Brain Germinal Matrix	brain
32	chr4:16212000-16220600	Weak transcription	A549	lung
33	chr4:16212200-16226000	Weak transcription	NHDF-Ad	bronchial
34	chr4:16213000-16221400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:16214000-16218800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr4:16214000-16218800	Weak transcription	Brain Substantia Nigra	brain
37	chr4:16214000-16224400	Weak transcription	Brain Anterior Caudate	brain
38	chr4:16214200-16219000	Weak transcription	HUVEC	blood vessel
39	chr4:16214200-16221800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr4:16214200-16224200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:16214400-16218600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr4:16214400-16218600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:16214400-16220800	Weak transcription	Fetal Stomach	stomach
44	chr4:16214400-16226800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr4:16214600-16222600	Weak transcription	Fetal Heart	heart
46	chr4:16214600-16224400	Weak transcription	Brain Angular Gyrus	brain
47	chr4:16214600-16225800	Weak transcription	Placenta	Placenta
48	chr4:16214800-16220800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr4:16214800-16224200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr4:16214800-16225200	Weak transcription	Hela-S3	cervix

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