Variant report

Variant	rs4235382
Chromosome Location	chr4:16225211-16225212
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr4:16224496-16225233	HepG2	liver:	n/a	n/a
2	EP300	chr4:16224473-16225233	HepG2	liver:	n/a	n/a
3	FOXA1	chr4:16224346-16225247	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:16224488-16225299	HepG2	liver:	n/a	n/a
5	FOXA2	chr4:16224942-16225211	HepG2	liver:	n/a	n/a
6	ARID3A	chr4:16224569-16225248	HepG2	liver:	n/a	n/a
7	JUND	chr4:16224502-16225254	HepG2	liver:	n/a	n/a
8	TEAD4	chr4:16224573-16225307	HepG2	liver:	n/a	n/a
9	MYBL2	chr4:16224467-16225373	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:16214985..16216532-chr4:16224088..16226157,2	K562	blood:
2	chr4:16221619..16226314-chr4:16226369..16230057,8	MCF-7	breast:
3	chr4:16207884..16210057-chr4:16223808..16226102,2	K562	blood:
4	chr4:16208002..16209532-chr4:16222968..16225755,2	MCF-7	breast:

No data

Variant related genes	Relation type
TAPT1-AS1	TF binding region
ENSG00000169762	Chromatin interaction
ENSG00000263327	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10017532	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10516297	0.81[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs11730922	0.82[ASN][1000 genomes]
rs13120908	0.86[ASN][1000 genomes]
rs13132678	0.85[ASN][1000 genomes]
rs13136172	0.88[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs13151111	0.85[AFR][1000 genomes]
rs1373109	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs2028631	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28496446	0.86[AFR][1000 genomes]
rs28654954	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28726676	0.83[AFR][1000 genomes]
rs33980476	0.88[CEU][hapmap];0.80[CHD][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs34129131	0.81[ASN][1000 genomes]
rs34496855	0.82[ASN][1000 genomes]
rs34592687	0.83[ASN][1000 genomes]
rs34663238	0.83[ASN][1000 genomes]
rs35475888	0.86[ASN][1000 genomes]
rs35517826	0.85[ASN][1000 genomes]
rs35804424	0.83[ASN][1000 genomes]
rs35806798	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35899968	0.83[ASN][1000 genomes]
rs35931597	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4481232	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4571326	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4698138	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4698457	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56353092	0.83[ASN][1000 genomes]
rs6810390	0.86[ASN][1000 genomes]
rs6852432	0.86[ASN][1000 genomes]
rs73798875	0.86[AFR][1000 genomes]
rs9995025	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv878720	chr4:16222046-16242215	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16193000-16225800	Weak transcription	Colonic Mucosa	Colon
2	chr4:16193200-16225800	Weak transcription	Fetal Brain Female	brain
3	chr4:16198800-16225600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:16198800-16226000	Weak transcription	NHEK	skin
5	chr4:16198800-16226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:16204800-16226600	Weak transcription	NH-A	brain
7	chr4:16205200-16225600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:16208400-16225800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:16208800-16225600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:16208800-16225600	Weak transcription	Esophagus	oesophagus
11	chr4:16208800-16225600	Weak transcription	Gastric	stomach
12	chr4:16208800-16225800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:16208800-16225800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:16208800-16227200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:16209000-16225600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:16209200-16225600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr4:16209200-16225600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:16209400-16226200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:16209400-16226200	Weak transcription	HSMMtube	muscle
20	chr4:16210400-16225800	Weak transcription	Brain Germinal Matrix	brain
21	chr4:16212200-16226000	Weak transcription	NHDF-Ad	bronchial
22	chr4:16214400-16226800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr4:16214600-16225800	Weak transcription	Placenta	Placenta
24	chr4:16214800-16225800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:16215000-16226000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:16215600-16225600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:16216200-16225600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:16216800-16225600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:16218600-16225600	Weak transcription	Lung	lung
30	chr4:16219600-16225600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr4:16221600-16225600	Weak transcription	Right Ventricle	heart
32	chr4:16221600-16225800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr4:16221800-16225400	Weak transcription	Right Atrium	heart
34	chr4:16221800-16225600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:16222200-16225600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr4:16222800-16225600	Weak transcription	Fetal Stomach	stomach
37	chr4:16222800-16226000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:16223000-16225600	Weak transcription	Pancreas	Pancrea
39	chr4:16223400-16225800	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr4:16223400-16225800	Enhancers	Adipose Nuclei	Adipose
41	chr4:16223400-16225800	Active TSS	GM12878-XiMat	blood
42	chr4:16223400-16226000	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr4:16223400-16226200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr4:16223600-16225600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr4:16223600-16225800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr4:16223600-16225800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr4:16223600-16225800	Enhancers	Brain Hippocampus Middle	brain
48	chr4:16223600-16226000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr4:16223800-16225600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr4:16223800-16225600	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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