Variant report

Variant	rs60866742
Chromosome Location	chr4:22457854-22457855
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	MYBL2	chr4:22457766-22458495	HepG2	liver:	n/a	n/a
2	HNF4A	chr4:22457845-22458371	HepG2	liver:	n/a	chr4:22458138-22458153
3	HNF4G	chr4:22457846-22458439	HepG2	liver:	n/a	chr4:22458139-22458154
4	FOXA1	chr4:22457820-22458438	HepG2	liver:	n/a	n/a
5	EP300	chr4:22457826-22458458	HepG2	liver:	n/a	n/a
6	HNF4A	chr4:22457849-22458389	HepG2	liver:	n/a	chr4:22458138-22458153
7	MYBL2	chr4:22457824-22458480	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:22457536..22463707-chr4:22514115..22518559,7	MCF-7	breast:

Variant related genes	Relation type
GPR125	TF binding region
ENSG00000152990	Chromatin interaction

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

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

rs_ID	r²[population]
rs12108612	0.89[AMR][1000 genomes]
rs2323410	0.89[AMR][1000 genomes]
rs55846611	0.82[AFR][1000 genomes]
rs58915823	0.89[AMR][1000 genomes]
rs59048448	0.89[AMR][1000 genomes]
rs59796925	0.89[AMR][1000 genomes]
rs73800942	0.87[AMR][1000 genomes]
rs73800943	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73800969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73802820	0.89[AMR][1000 genomes]
rs73802826	0.89[AMR][1000 genomes]
rs73802828	0.89[AMR][1000 genomes]
rs73802837	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv878752	chr4:22414023-22501043	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv821634	chr4:22427074-22865948	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22388400-22473600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:22388800-22469600	Weak transcription	Colonic Mucosa	Colon
3	chr4:22389200-22473600	Weak transcription	Fetal Brain Male	brain
4	chr4:22390600-22459800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr4:22393600-22459800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:22400800-22461800	Weak transcription	Gastric	stomach
7	chr4:22419200-22476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:22419400-22465800	Weak transcription	HUVEC	blood vessel
9	chr4:22420600-22488000	Weak transcription	Aorta	Aorta
10	chr4:22426000-22461800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:22428600-22460600	Weak transcription	Placenta	Placenta
12	chr4:22432400-22460400	Weak transcription	Small Intestine	intestine
13	chr4:22433800-22479200	Weak transcription	Brain Hippocampus Middle	brain
14	chr4:22434000-22461200	Weak transcription	Brain Anterior Caudate	brain
15	chr4:22437400-22476400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:22437800-22459600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr4:22437800-22465000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr4:22439200-22458000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:22443400-22471200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:22443400-22472400	Weak transcription	Ovary	ovary
21	chr4:22443400-22473600	Weak transcription	Fetal Brain Female	brain
22	chr4:22443600-22470800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:22443600-22476200	Weak transcription	A549	lung
24	chr4:22443800-22474600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:22444000-22470800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr4:22447200-22467600	Weak transcription	Thymus	Thymus
27	chr4:22447200-22473800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr4:22447200-22475000	Weak transcription	NHLF	lung
29	chr4:22447800-22473400	Weak transcription	Brain Germinal Matrix	brain
30	chr4:22448000-22461400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:22448600-22472600	Weak transcription	Primary T cells from cord blood	blood
32	chr4:22449600-22458200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr4:22450200-22459600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:22450200-22471000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:22450200-22473800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr4:22450200-22473800	Weak transcription	NH-A	brain
37	chr4:22450400-22460200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:22450400-22461800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr4:22450400-22474800	Weak transcription	Adipose Nuclei	Adipose
40	chr4:22450400-22476000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:22450400-22484000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr4:22450400-22493200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:22450800-22464200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:22451200-22459600	Weak transcription	Liver	Liver
45	chr4:22451400-22464000	Weak transcription	Fetal Stomach	stomach
46	chr4:22453400-22458600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr4:22453400-22460800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:22453800-22460000	Weak transcription	Psoas Muscle	Psoas
49	chr4:22454400-22462200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr4:22455600-22474200	Weak transcription	Fetal Thymus	thymus

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