Variant report

Variant	rs28651722
Chromosome Location	chr4:57279469-57279470
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	POLR2A	chr4:57279436-57279547	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57277811..57280010-chr4:57300306..57302094,2	MCF-7	breast:
2	chr4:57252177..57255146-chr4:57278604..57280682,2	MCF-7	breast:
3	chr4:57278722..57280888-chr4:57296778..57299271,2	MCF-7	breast:
4	chr4:57273341..57278355-chr4:57278652..57283436,7	K562	blood:

Variant related genes	Relation type
PPAT	TF binding region
ENSG00000268171	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000269921	Chromatin interaction
ENSG00000128059	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10003484	1.00[AFR][1000 genomes]
rs10007966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28501253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28552845	1.00[AFR][1000 genomes]
rs28558611	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28623333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28632116	1.00[AMR][1000 genomes]
rs28653752	1.00[AFR][1000 genomes]
rs9994079	1.00[AFR][1000 genomes]
rs9994575	1.00[AMR][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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv4347	chr4:57261404-57280595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1801975	chr4:57267406-57297335	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:57264200-57290200	Weak transcription	Esophagus	oesophagus
4	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:57272600-57280200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:57272800-57280400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:57272800-57281600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:57272800-57292600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:57272800-57299800	Weak transcription	Primary T cells from cord blood	blood
11	chr4:57272800-57299800	Weak transcription	Fetal Thymus	thymus
12	chr4:57272800-57300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:57274000-57287000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:57274000-57290600	Weak transcription	GM12878-XiMat	blood
15	chr4:57274200-57287000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:57274200-57296400	Weak transcription	Dnd41	blood
17	chr4:57276200-57280200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:57276800-57284200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:57277000-57280200	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:57277000-57280200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr4:57277000-57280400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:57277000-57287200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:57277000-57287200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:57277000-57287400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:57277000-57289800	Weak transcription	Fetal Stomach	stomach
26	chr4:57277000-57290000	Weak transcription	Aorta	Aorta
27	chr4:57277000-57290200	Weak transcription	Ovary	ovary
28	chr4:57277000-57290800	Weak transcription	Right Atrium	heart
29	chr4:57277000-57294200	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:57277000-57299200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:57277000-57300000	Weak transcription	HSMM	muscle
32	chr4:57277200-57280200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:57277200-57280200	Weak transcription	HMEC	breast
34	chr4:57277200-57280400	Weak transcription	NH-A	brain
35	chr4:57277200-57283000	Weak transcription	Fetal Intestine Small	intestine
36	chr4:57277800-57280000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:57277800-57280000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:57277800-57280200	Weak transcription	NHLF	lung
39	chr4:57277800-57280400	Weak transcription	Fetal Lung	lung
40	chr4:57277800-57298000	Weak transcription	A549	lung
41	chr4:57278000-57280200	Weak transcription	Osteobl	bone
42	chr4:57278000-57286800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:57278000-57286800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:57278000-57290400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr4:57278000-57291600	Weak transcription	Brain Anterior Caudate	brain
46	chr4:57278000-57291600	Weak transcription	HepG2	liver
47	chr4:57278000-57294000	Weak transcription	HUVEC	blood vessel
48	chr4:57278000-57299200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:57278200-57280200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr4:57278200-57280400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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