Variant report

Variant	rs28689013
Chromosome Location	chr4:79699129-79699130
allele	G/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	EP300	chr4:79699004-79699377	K562	blood:	n/a	n/a
2	POLR2A	chr4:79695600-79704800	PBDE	blood:	n/a	n/a
3	POLR2A	chr4:79696044-79699275	MCF10A-Er-Src	breast:	n/a	n/a
4	MXI1	chr4:79699022-79699426	GM12878	blood:	n/a	n/a
5	IRF1	chr4:79698043-79700891	K562	blood:	n/a	chr4:79699678-79699685 chr4:79698149-79698158 chr4:79699001-79699011 chr4:79698997-79699011 chr4:79699699-79699716
6	MAX	chr4:79699116-79699417	NB4	blood:	n/a	chr4:79699239-79699249
7	POLR2A	chr4:79697963-79699280	K562	blood:	n/a	n/a
8	IRF1	chr4:79698350-79699734	K562	blood:	n/a	chr4:79699678-79699685 chr4:79699001-79699011 chr4:79698997-79699011 chr4:79699699-79699716
9	TBL1XR1	chr4:79698151-79701864	K562	blood:	n/a	n/a
10	MYC	chr4:79699086-79699418	MCF10A-Er-Src	breast:	n/a	chr4:79699239-79699249
11	EP300	chr4:79699058-79699257	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:79522193..79524527-chr4:79697309..79699707,2	MCF-7	breast:
2	chr4:79591975..79594296-chr4:79697576..79699186,2	K562	blood:
3	chr4:79570295..79572982-chr4:79695014..79699413,6	MCF-7	breast:
4	chr4:79562196..79569044-chr4:79695847..79699797,11	MCF-7	breast:
5	chr4:79548752..79551333-chr4:79698595..79700948,2	K562	blood:
6	chr4:79697257..79699576-chr4:79770892..79773352,2	MCF-7	breast:
7	chr4:79568346..79573757-chr4:79695931..79699478,7	MCF-7	breast:
8	chr4:79563120..79566472-chr4:79698388..79700680,4	K562	blood:
9	chr4:79557978..79560128-chr4:79697718..79699238,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260278	TF binding region
ENSG00000251019	Chromatin interaction
ENSG00000138772	Chromatin interaction
ENSG00000138756	Chromatin interaction
ENSG00000251442	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10011360	1.00[AMR][1000 genomes]
rs10022801	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028888	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10031149	1.00[AMR][1000 genomes]
rs10032333	1.00[AMR][1000 genomes]
rs10033281	1.00[AMR][1000 genomes]
rs10440396	1.00[AMR][1000 genomes]
rs10440397	1.00[AMR][1000 genomes]
rs10518203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10518204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17003461	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28366415	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28377257	1.00[AMR][1000 genomes]
rs28423984	1.00[AMR][1000 genomes]
rs28440150	1.00[AMR][1000 genomes]
rs28451964	1.00[AMR][1000 genomes]
rs28452521	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28456317	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28479356	1.00[AMR][1000 genomes]
rs28551149	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28580580	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28674732	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28676399	1.00[AMR][1000 genomes]
rs28681258	1.00[AMR][1000 genomes]
rs28705943	1.00[AMR][1000 genomes]
rs28708661	1.00[AMR][1000 genomes]
rs28708924	1.00[AMR][1000 genomes]
rs28709346	1.00[AMR][1000 genomes]
rs28722195	1.00[AMR][1000 genomes]
rs28781350	1.00[AMR][1000 genomes]
rs28818508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28896313	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9991385	1.00[AMR][1000 genomes]
rs9991672	1.00[AMR][1000 genomes]
rs9994104	1.00[AMR][1000 genomes]
rs9995485	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1803379	chr4:79661618-79704210	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv1792021	chr4:79661618-79784245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
3	esv3358831	chr4:79696153-79699301	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv1792429	chr4:79697116-79704210	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv1798320	chr4:79697116-79704210	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv1801852	chr4:79697116-79704210	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv1802642	chr4:79697116-79704210	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv1802703	chr4:79697116-79704210	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	esv1833723	chr4:79697116-79704210	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	esv1833992	chr4:79697116-79704210	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	esv1835474	chr4:79697116-79704210	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	esv1837381	chr4:79697116-79704210	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	esv1845915	chr4:79697116-79704210	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79696000-79699600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:79696000-79699800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:79696200-79699200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr4:79696200-79699200	Active TSS	H1 Cell Line	embryonic stem cell
5	chr4:79696200-79699200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:79696200-79699200	Active TSS	Fetal Kidney	kidney
7	chr4:79696200-79699200	Active TSS	Fetal Muscle Trunk	muscle
8	chr4:79696200-79699200	Active TSS	Fetal Stomach	stomach
9	chr4:79696200-79699200	Active TSS	Psoas Muscle	Psoas
10	chr4:79696200-79699600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:79696200-79699600	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr4:79696200-79699600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:79696200-79699800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:79696200-79699800	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr4:79696200-79699800	Active TSS	Thymus	Thymus
16	chr4:79696200-79699800	Active TSS	NHDF-Ad	bronchial
17	chr4:79696200-79700200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:79696200-79700800	Active TSS	Rectal Smooth Muscle	rectum
19	chr4:79696400-79699200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:79696400-79699200	Active TSS	Right Ventricle	heart
21	chr4:79696400-79699400	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr4:79696400-79699400	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr4:79696400-79699400	Active TSS	GM12878-XiMat	blood
24	chr4:79696400-79700000	Active TSS	K562	blood
25	chr4:79696400-79700800	Active TSS	Fetal Intestine Small	intestine
26	chr4:79696600-79699600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:79696600-79699600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:79696600-79699800	Active TSS	HSMMtube	muscle
29	chr4:79696600-79700600	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr4:79696600-79700600	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr4:79696600-79701000	Active TSS	Fetal Intestine Large	intestine
32	chr4:79696600-79701000	Active TSS	NHLF	lung
33	chr4:79696800-79699400	Active TSS	Fetal Thymus	thymus
34	chr4:79696800-79699600	Active TSS	Primary B cells from peripheral blood	blood
35	chr4:79696800-79699600	Active TSS	HMEC	breast
36	chr4:79697400-79699600	Active TSS	Brain Germinal Matrix	brain
37	chr4:79697600-79700800	Active TSS	Right Atrium	heart
38	chr4:79697800-79699200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr4:79698000-79700600	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr4:79698200-79699200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr4:79698200-79699200	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr4:79698200-79699600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:79698200-79699600	Flanking Active TSS	NH-A	brain
44	chr4:79698200-79700200	Flanking Active TSS	HUVEC	blood vessel
45	chr4:79698200-79700800	Flanking Active TSS	Dnd41	blood
46	chr4:79698200-79701200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr4:79698400-79699200	Active TSS	Stomach Smooth Muscle	stomach
48	chr4:79698400-79699400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:79698400-79700400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:79698600-79699200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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