Variant report

Variant	rs72870619
Chromosome Location	chr4:87514915-87514916
allele	C/T
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	SIN3A	chr4:87514658-87516665	H1-hESC	embryonic stem cell:	n/a	chr4:87515808-87515819 chr4:87515790-87515798 chr4:87516285-87516298 chr4:87516291-87516299 chr4:87515437-87515450
2	POLR2A	chr4:87514820-87515809	U87	brain:	n/a	n/a
3	MYC	chr4:87514875-87516629	NB4	blood:	n/a	chr4:87516065-87516074 chr4:87516469-87516478
4	POLR2A	chr4:87514869-87515893	GM12878	blood:	n/a	n/a
5	MAX	chr4:87514908-87515919	A549	lung:	n/a	n/a
6	CUX1	chr4:87514731-87515536	GM12878	blood:	n/a	n/a
7	MXI1	chr4:87514804-87517131	IMR90	lung:	n/a	chr4:87515287-87515302
8	REST	chr4:87514755-87516530	H1-neurons	neurons:	n/a	chr4:87516285-87516298 chr4:87515437-87515450 chr4:87515440-87515453 chr4:87515278-87515288 chr4:87515791-87515799 chr4:87515557-87515570
9	RFX5	chr4:87513354-87517357	SK-N-SH	brain:	n/a	chr4:87517101-87517110 chr4:87515266-87515281 chr4:87515341-87515350
10	MAZ	chr4:87514856-87516888	IMR90	lung:	n/a	chr4:87516065-87516074 chr4:87516469-87516478
11	E2F6	chr4:87514895-87515725	H1-hESC	embryonic stem cell:	n/a	chr4:87515431-87515440 chr4:87515661-87515670
12	SP1	chr4:87514792-87515676	A549	lung:	n/a	chr4:87515313-87515327 chr4:87515423-87515432 chr4:87515421-87515433 chr4:87515339-87515360 chr4:87515421-87515433 chr4:87515418-87515432 chr4:87515421-87515432 chr4:87515422-87515431
13	CHD2	chr4:87514885-87516443	GM12878	blood:	n/a	n/a
14	SP4	chr4:87514825-87515605	H1-hESC	embryonic stem cell:	n/a	chr4:87515419-87515435 chr4:87515417-87515433 chr4:87515421-87515432
15	FOXM1	chr4:87514878-87515723	GM12878	blood:	n/a	n/a
16	NFIC	chr4:87514788-87515800	GM12878	blood:	n/a	n/a
17	MYC	chr4:87514784-87515673	MCF10A-Er-Src	breast:	n/a	n/a
18	RUNX3	chr4:87514794-87516796	GM12878	blood:	n/a	n/a
19	EBF1	chr4:87514573-87515669	GM12878	blood:	n/a	chr4:87515306-87515316 chr4:87515305-87515318 chr4:87515307-87515316 chr4:87515307-87515317 chr4:87515305-87515316
20	ZNF263	chr4:87514910-87516854	HEK293-T-REx	kidney:	n/a	chr4:87515313-87515334 chr4:87515312-87515321 chr4:87515738-87515747 chr4:87515741-87515750 chr4:87515735-87515744
21	MAX	chr4:87514870-87515590	H1-hESC	embryonic stem cell:	n/a	n/a
22	YY1	chr4:87514738-87515251	H1-hESC	embryonic stem cell:	n/a	n/a
23	TAF1	chr4:87514752-87516019	H1-hESC	embryonic stem cell:	n/a	n/a
24	SMC3	chr4:87514899-87515659	GM12878	blood:	n/a	n/a
25	RAD21	chr4:87514808-87515677	GM12878	blood:	n/a	chr4:87515474-87515487
26	MXI1	chr4:87514817-87515680	H1-hESC	embryonic stem cell:	n/a	chr4:87515287-87515302
27	CHD1	chr4:87514635-87515101	H1-hESC	embryonic stem cell:	n/a	n/a
28	YY1	chr4:87514802-87515223	GM12878	blood:	n/a	n/a
29	POLR2A	chr4:87514889-87516121	H1-neurons	neurons:	n/a	n/a
30	EBF1	chr4:87514728-87515691	GM12878	blood:	n/a	chr4:87515306-87515316 chr4:87515305-87515318 chr4:87515307-87515316 chr4:87515307-87515317 chr4:87515305-87515316
31	POLR2A	chr4:87513750-87517480	MCF10A-Er-Src	breast:	n/a	n/a
32	RFX5	chr4:87514798-87515449	H1-hESC	embryonic stem cell:	n/a	chr4:87515266-87515281 chr4:87515341-87515350
33	POLR2A	chr4:87514798-87515752	GM12878	blood:	n/a	n/a
34	CEBPB	chr4:87514710-87515223	GM12878	blood:	n/a	n/a
35	RAD21	chr4:87514884-87516540	SK-N-SH_RA	brain:	n/a	chr4:87515812-87515826 chr4:87515474-87515487
36	MAX	chr4:87514747-87516554	A549	lung:	n/a	chr4:87516065-87516074 chr4:87516469-87516478
37	POLR2A	chr4:87514714-87517094	SK-N-MC	brain:	n/a	n/a
38	MXI1	chr4:87514565-87516730	GM12878	blood:	n/a	chr4:87515287-87515302
39	TAF1	chr4:87514732-87516584	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr4:87514755-87515664	SK-N-MC	brain:	n/a	n/a
41	POLR2A	chr4:87514860-87515759	GM12878	blood:	n/a	n/a
42	PML	chr4:87514794-87516691	GM12878	blood:	n/a	n/a
43	YY1	chr4:87514757-87515255	H1-hESC	embryonic stem cell:	n/a	n/a
44	MYC	chr4:87514605-87515127	MCF10A-Er-Src	breast:	n/a	n/a
45	REST	chr4:87514769-87515728	A549	lung:	n/a	chr4:87515437-87515450 chr4:87515440-87515453 chr4:87515278-87515288 chr4:87515557-87515570
46	MXI1	chr4:87514222-87517185	SK-N-SH	brain:	n/a	chr4:87515287-87515302
47	EBF1	chr4:87514087-87515806	GM12878	blood:	n/a	chr4:87515306-87515316 chr4:87515305-87515318 chr4:87515307-87515316 chr4:87515307-87515317 chr4:87515305-87515316
48	POLR2A	chr4:87514656-87517155	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr4:87514890-87515784	GM12891	blood:	n/a	n/a
50	SP1	chr4:87514812-87515572	H1-hESC	embryonic stem cell:	n/a	chr4:87515313-87515327 chr4:87515423-87515432 chr4:87515421-87515433 chr4:87515339-87515360 chr4:87515421-87515433 chr4:87515418-87515432 chr4:87515421-87515432 chr4:87515422-87515431

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:87514906-87514956	AG09319	gingival:	n/a
2	chr4:87514906-87514956	MCF-7	breast:	n/a
3	chr4:87514906-87514956	K562	blood:	n/a
4	chr4:87514906-87514956	IMR90	lung:	fetal
5	chr4:87514906-87514956	HEEpiC	esophagus:	n/a
6	chr4:87514906-87514956	AG04449	skin:	fetal
7	chr4:87514906-87514956	HRPEpiC	eye:	n/a
8	chr4:87514906-87514956	H1-hESC	embryonic stem cell:	embryo
9	chr4:87514906-87514956	PFSK-1	brain:	n/a
10	chr4:87514906-87514956	HCT-116	colon:	n/a
11	chr4:87514906-87514956	HIPEpiC	eye:	n/a
12	chr4:87514906-87514956	HepG2	liver:	n/a
13	chr4:87514906-87514956	HCM	heart:	n/a
14	chr4:87514906-87514956	HNPCEpiC	eye:	n/a
15	chr4:87514906-87514956	HCF	heart:	n/a
16	chr4:87514906-87514956	SK-N-SH	brain:	n/a
17	chr4:87514906-87514956	LNCaP	prostate:	n/a
18	chr4:87514906-87514956	BJ	skin:	n/a
19	chr4:87514906-87514956	SK-N-SH_RA	brain:	n/a
20	chr4:87514906-87514956	HMEC	breast:	n/a
21	chr4:87514906-87514956	Jurkat	blood:	n/a
22	chr4:87514906-87514956	HPAEpiC	pulmonary alveolar:	n/a
23	chr4:87514906-87514956	A549	lung:	n/a
24	chr4:87514906-87514956	ECC-1	luminal epithelium:	n/a
25	chr4:87514906-87514956	SAEC	small airway:	n/a
26	chr4:87514906-87514956	U87	brain:	n/a
27	chr4:87514906-87514956	HUVEC	blood vessel:	n/a
28	chr4:87514906-87514956	HRE	kidney:	n/a
29	chr4:87514906-87514956	MCF10A-Er-Src	breast:	n/a
30	chr4:87514906-87514956	NHBE	bronchial:	n/a
31	chr4:87514906-87514956	PANC-1	pancreas:	n/a
32	chr4:87514906-87514956	RPTEC	kidney:	n/a
33	chr4:87514906-87514956	BE2_C	brain:	n/a
34	chr4:87514906-87514956	HL-60	blood:	n/a
35	chr4:87514906-87514956	AG10803	skin:	n/a
36	chr4:87514906-87514956	AG09309	skin:	n/a
37	chr4:87514906-87514956	GM12878	blood:	n/a
38	chr4:87514906-87514956	CMK	blood:	n/a
39	chr4:87514906-87514956	Hela-S3	cervix:	n/a
40	chr4:87514906-87514956	HEK293	kidney:	embryo
41	chr4:87514906-87514956	Hepatocyte	liver:	n/a
42	chr4:87514906-87514956	AG04450	lung:	fetal
43	chr4:87514906-87514956	GM12892	blood:	n/a
44	chr4:87514906-87514956	HRCEpiC	kidney:	n/a
45	chr4:87514906-87514956	SKMC	muscle:	n/a
46	chr4:87514906-87514956	GM06990	blood:	n/a
47	chr4:87514906-87514956	GM12891	blood:	n/a
48	chr4:87514906-87514956	NB4	blood:	n/a
49	chr4:87514906-87514956	T-47D	breast:	n/a
50	chr4:87514906-87514956	Caco-2	colon:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87507433..87508945-chr4:87512741..87515141,2	MCF-7	breast:
2	chr4:87514124..87517809-chr4:87811943..87814768,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC10A6-4	chr4:87514886-87515272	NONHSAT097281

Variant related genes	Relation type
PTPN13	TF binding region
PTPN13	CpG island
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs59285334	1.00[AFR][1000 genomes]
rs72868848	1.00[AFR][1000 genomes]
rs72868852	1.00[AFR][1000 genomes]
rs72868855	1.00[AFR][1000 genomes]
rs72868861	1.00[AFR][1000 genomes]
rs72868865	1.00[AFR][1000 genomes]
rs72868868	1.00[AFR][1000 genomes]
rs72868878	1.00[AFR][1000 genomes]
rs72868880	1.00[AFR][1000 genomes]
rs72868881	1.00[AFR][1000 genomes]
rs72868883	1.00[AFR][1000 genomes]
rs72868884	1.00[AFR][1000 genomes]
rs72870634	1.00[AFR][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	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv879522	chr4:87473776-87644842	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv822635	chr4:87479576-87622176	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87513200-87518000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:87513200-87518600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:87513400-87515000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr4:87513400-87517400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:87513600-87517400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr4:87513600-87518000	Active TSS	H1 Cell Line	embryonic stem cell
7	chr4:87513600-87518400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:87513800-87515000	Flanking Active TSS	Osteobl	bone
9	chr4:87513800-87515200	Flanking Active TSS	NH-A	brain
10	chr4:87513800-87515600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:87513800-87517000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:87513800-87517800	Active TSS	Brain Anterior Caudate	brain
13	chr4:87513800-87518400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr4:87514000-87515000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:87514000-87515200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:87514000-87516200	Active TSS	Fetal Brain Female	brain
17	chr4:87514000-87517400	Active TSS	A549	lung
18	chr4:87514000-87518600	Active TSS	Fetal Kidney	kidney
19	chr4:87514000-87519000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:87514200-87515000	Active TSS	Brain Germinal Matrix	brain
21	chr4:87514200-87517200	Active TSS	H9 Cell Line	embryonic stem cell
22	chr4:87514200-87517400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr4:87514200-87517800	Active TSS	Brain Angular Gyrus	brain
24	chr4:87514400-87515200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:87514400-87517000	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr4:87514400-87517400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:87514400-87517600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:87514400-87518400	Active TSS	Right Atrium	heart
29	chr4:87514600-87515000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr4:87514600-87515000	Flanking Active TSS	Fetal Stomach	stomach
31	chr4:87514600-87515200	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr4:87514600-87515200	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr4:87514600-87515400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:87514600-87516600	Active TSS	Fetal Heart	heart
35	chr4:87514600-87517000	Active TSS	Colon Smooth Muscle	Colon
36	chr4:87514600-87517200	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr4:87514600-87517200	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr4:87514600-87517200	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr4:87514600-87517200	Active TSS	NHLF	lung
40	chr4:87514600-87517600	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr4:87514600-87517600	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr4:87514600-87518000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:87514600-87518200	Active TSS	NHDF-Ad	bronchial
44	chr4:87514600-87518200	Active TSS	NHEK	skin
45	chr4:87514600-87518800	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr4:87514800-87515000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr4:87514800-87515000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:87514800-87515000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
49	chr4:87514800-87515000	Active TSS	Primary T cells from cord blood	blood
50	chr4:87514800-87515000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood

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