Variant report

Variant	rs59008728
Chromosome Location	chr4:87926408-87926409
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr4:87926346-87929776	GM12878	blood:	n/a	chr4:87929083-87929094 chr4:87929086-87929100 chr4:87929083-87929103 chr4:87929082-87929097 chr4:87929085-87929101
2	POLR2A	chr4:87925639-87929947	K562	blood:	n/a	n/a
3	ATF2	chr4:87926407-87927272	GM12878	blood:	n/a	n/a
4	RELA	chr4:87926273-87929243	GM15510	blood:	n/a	n/a
5	NFIC	chr4:87926406-87928901	GM12878	blood:	n/a	n/a
6	POLR2A	chr4:87926259-87929411	Hela-S3	cervix:	n/a	n/a
7	MAX	chr4:87926405-87926494	GM12878	blood:	n/a	n/a
8	BCLAF1	chr4:87926328-87928894	GM12878	blood:	n/a	n/a
9	BATF	chr4:87926235-87926606	GM12878	blood:	n/a	n/a
10	PML	chr4:87926388-87929113	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:87926218-87929356	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:87926128-87929792	GM12891	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:87925728..87928090-chr4:88141264..88142892,2	MCF-7	breast:
2	chr4:87851729..87853326-chr4:87926399..87928104,2	MCF-7	breast:
3	chr4:87925271..87927953-chr4:88006288..88008752,2	K562	blood:
4	chr4:87925271..87928107-chr4:88005926..88008504,3	K562	blood:
5	chr4:87906409..87908323-chr4:87926209..87928101,2	MCF-7	breast:
6	chr4:87926172..87928696-chr7:150019642..150022141,2	MCF-7	breast:
7	chr4:87845889..87863516-chr4:87925389..87935181,79	K562	blood:
8	chr4:87853395..87861870-chr4:87925425..87930611,18	MCF-7	breast:
9	chr4:87926199..87928138-chr4:87938575..87940535,2	MCF-7	breast:
10	chr4:87925170..87928506-chr4:88140421..88143207,4	MCF-7	breast:
11	chr4:87854708..87860113-chr4:87926348..87930107,23	MCF-7	breast:
12	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:
13	chr4:87925063..87927855-chr4:88154539..88157120,2	MCF-7	breast:

No data

Variant related genes	Relation type
AFF1	TF binding region
ENSG00000235043	Chromatin interaction
ENSG00000145332	Chromatin interaction
ENSG00000172493	Chromatin interaction
ENSG00000163633	Chromatin interaction
ENSG00000106526	Chromatin interaction
ENSG00000127399	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs59154061	1.00[AFR][1000 genomes]
rs61734711	1.00[AFR][1000 genomes]
rs72876004	1.00[AFR][1000 genomes]
rs72876032	1.00[AFR][1000 genomes]
rs72876056	1.00[AFR][1000 genomes]
rs72877906	1.00[AFR][1000 genomes]
rs72877914	1.00[AFR][1000 genomes]
rs72877990	1.00[AFR][1000 genomes]
rs72879911	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	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87899200-87926600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:87914200-87927400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:87916200-87927200	Weak transcription	Esophagus	oesophagus
4	chr4:87916400-87927200	Weak transcription	Gastric	stomach
5	chr4:87919000-87927000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr4:87919200-87927400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:87921200-87927000	Weak transcription	Right Ventricle	heart
8	chr4:87921800-87926600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:87921800-87926600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:87922000-87926600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:87922200-87926600	Weak transcription	Adipose Nuclei	Adipose
12	chr4:87922400-87927000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr4:87923000-87926600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:87923200-87927200	Weak transcription	Ovary	ovary
15	chr4:87923400-87926600	Weak transcription	Brain Anterior Caudate	brain
16	chr4:87923600-87926600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:87924600-87927000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:87924600-87927400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:87924800-87926800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:87925200-87926600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:87925200-87927400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr4:87925400-87926600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:87925400-87926800	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr4:87925400-87927000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:87925800-87926600	Enhancers	Primary B cells from cord blood	blood
26	chr4:87925800-87926600	Enhancers	Primary T cells from cord blood	blood
27	chr4:87925800-87926600	Enhancers	Primary hematopoietic stem cells	blood
28	chr4:87925800-87926600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr4:87925800-87926600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr4:87925800-87926800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:87925800-87926800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:87925800-87926800	Enhancers	Brain Hippocampus Middle	brain
33	chr4:87925800-87926800	Enhancers	Hela-S3	cervix
34	chr4:87926000-87926600	Enhancers	HepG2	liver
35	chr4:87926000-87926600	Enhancers	NHLF	lung
36	chr4:87926000-87926800	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr4:87926000-87926800	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr4:87926000-87926800	Enhancers	Primary T cells fromperipheralblood	blood
39	chr4:87926000-87926800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr4:87926000-87926800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr4:87926000-87927000	Enhancers	A549	lung
42	chr4:87926000-87927600	Flanking Active TSS	GM12878-XiMat	blood
43	chr4:87926200-87926600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:87926200-87926600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:87926200-87926600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:87926200-87926600	Enhancers	Colon Smooth Muscle	Colon
47	chr4:87926200-87926600	Enhancers	Duodenum Mucosa	Duodenum
48	chr4:87926200-87926600	Enhancers	Fetal Thymus	thymus
49	chr4:87926200-87926600	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr4:87926200-87926600	Enhancers	Thymus	Thymus

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