Variant report

Variant	rs72870617
Chromosome Location	chr4:87514199-87514200
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	EP300	chr4:87514046-87514355	SK-N-SH_RA	brain:	n/a	chr4:87514253-87514261
2	FOSL2	chr4:87513941-87514463	A549	lung:	n/a	n/a
3	EP300	chr4:87514074-87514465	SK-N-SH_RA	brain:	n/a	chr4:87514253-87514261
4	POLR2A	chr4:87513978-87514355	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr4:87513838-87514583	SK-N-SH	brain:	n/a	n/a
6	RFX5	chr4:87513354-87517357	SK-N-SH	brain:	n/a	chr4:87517101-87517110 chr4:87515266-87515281 chr4:87515341-87515350
7	PBX3	chr4:87513968-87514589	SK-N-SH	brain:	n/a	n/a
8	FOS	chr4:87514038-87514343	MCF10A-Er-Src	breast:	n/a	n/a
9	FOSL2	chr4:87514013-87514319	A549	lung:	n/a	n/a
10	FOS	chr4:87514098-87514330	MCF10A-Er-Src	breast:	n/a	n/a
11	TCF12	chr4:87513888-87514539	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr4:87513828-87514606	SK-N-SH	brain:	n/a	n/a
13	NFIC	chr4:87513877-87514504	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr4:87513878-87514493	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr4:87513750-87517480	MCF10A-Er-Src	breast:	n/a	n/a
16	FOSL2	chr4:87514001-87514409	SK-N-SH	brain:	n/a	n/a
17	TEAD4	chr4:87513862-87514402	A549	lung:	n/a	n/a
18	GATA3	chr4:87513829-87514644	A549	lung:	n/a	n/a
19	JUND	chr4:87513951-87514257	H1-hESC	embryonic stem cell:	n/a	n/a
20	FOS	chr4:87514021-87514364	MCF10A-Er-Src	breast:	n/a	n/a
21	EBF1	chr4:87514087-87515806	GM12878	blood:	n/a	chr4:87515306-87515316 chr4:87515305-87515318 chr4:87515307-87515316 chr4:87515307-87515317 chr4:87515305-87515316
22	FOS	chr4:87514011-87514421	MCF10A-Er-Src	breast:	n/a	n/a
23	JUND	chr4:87513873-87514581	SK-N-SH	brain:	n/a	n/a
24	JUND	chr4:87513912-87514508	SK-N-SH	brain:	n/a	n/a
25	EP300	chr4:87513937-87514509	SK-N-SH	brain:	n/a	chr4:87514253-87514261
26	PBX3	chr4:87513899-87514526	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:87507433..87508945-chr4:87512741..87515141,2	MCF-7	breast:
2	chr4:30768208..30768709-chr4:87513954..87514454,2	HCT-116	colon:
3	chr4:87507143..87508934-chr4:87512831..87514813,2	MCF-7	breast:
4	chr4:87514124..87517809-chr4:87811943..87814768,5	MCF-7	breast:

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

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11929807	1.00[AMR][1000 genomes]
rs11933110	1.00[AMR][1000 genomes]
rs11936622	1.00[AMR][1000 genomes]
rs11937511	1.00[AMR][1000 genomes]
rs11937815	1.00[AMR][1000 genomes]
rs11938746	1.00[AMR][1000 genomes]
rs11940149	1.00[AMR][1000 genomes]
rs11944714	1.00[AMR][1000 genomes]
rs11945220	1.00[AMR][1000 genomes]
rs61391256	1.00[AMR][1000 genomes]
rs61757791	1.00[AMR][1000 genomes]
rs6821849	1.00[AMR][1000 genomes]
rs72868898	1.00[AMR][1000 genomes]
rs72870603	1.00[AMR][1000 genomes]
rs72870604	1.00[AMR][1000 genomes]
rs7698902	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87502400-87514200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr4:87507600-87514200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:87508800-87514400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr4:87508800-87514600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:87512800-87514800	Weak transcription	Pancreas	Pancrea
6	chr4:87513000-87514800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:87513200-87514800	Weak transcription	Lung	lung
8	chr4:87513200-87518000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:87513200-87518600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:87513400-87514200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr4:87513400-87514200	Enhancers	Brain Angular Gyrus	brain
12	chr4:87513400-87514600	Flanking Active TSS	NHEK	skin
13	chr4:87513400-87514800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:87513400-87514800	Enhancers	Brain Substantia Nigra	brain
15	chr4:87513400-87515000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr4:87513400-87517400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:87513600-87514200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr4:87513600-87514200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr4:87513600-87514400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr4:87513600-87514400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:87513600-87514400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr4:87513600-87514600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr4:87513600-87514600	Enhancers	Adipose Nuclei	Adipose
24	chr4:87513600-87514800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:87513600-87514800	Flanking Active TSS	HMEC	breast
26	chr4:87513600-87517400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr4:87513600-87518000	Active TSS	H1 Cell Line	embryonic stem cell
28	chr4:87513600-87518400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:87513800-87514200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:87513800-87514200	Enhancers	Placenta Amnion	Placenta Amnion
31	chr4:87513800-87514400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:87513800-87514600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr4:87513800-87514600	Enhancers	Brain Hippocampus Middle	brain
34	chr4:87513800-87514600	Flanking Active TSS	NHLF	lung
35	chr4:87513800-87514800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr4:87513800-87514800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:87513800-87514800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr4:87513800-87515000	Flanking Active TSS	Osteobl	bone
39	chr4:87513800-87515200	Flanking Active TSS	NH-A	brain
40	chr4:87513800-87515600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:87513800-87517000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:87513800-87517800	Active TSS	Brain Anterior Caudate	brain
43	chr4:87513800-87518400	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr4:87514000-87514200	Flanking Active TSS	H9 Cell Line	embryonic stem cell
45	chr4:87514000-87514200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:87514000-87514200	Bivalent/Poised TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr4:87514000-87514200	Active TSS	Stomach Smooth Muscle	stomach
48	chr4:87514000-87514200	Enhancers	HSMMtube	muscle
49	chr4:87514000-87514400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:87514000-87514400	Enhancers	Fetal Lung	lung

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