Variant report

Variant	rs28698249
Chromosome Location	chr4:22459681-22459682
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	EP300	chr4:22459657-22460306	ECC-1	luminal epithelium:	n/a	n/a
2	GATA3	chr4:22459004-22459904	SK-N-SH	brain:	n/a	chr4:22459682-22459693

No.	Distal block	Cell Line	Cell type
1	chr4:22452403..22454410-chr4:22458067..22459809,2	MCF-7	breast:
2	chr4:22457536..22463707-chr4:22514115..22518559,7	MCF-7	breast:
3	chr4:22449726..22452368-chr4:22458347..22461364,3	MCF-7	breast:

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

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10000829	1.00[EUR][1000 genomes]
rs10004678	1.00[EUR][1000 genomes]
rs10006549	1.00[EUR][1000 genomes]
rs10012247	1.00[EUR][1000 genomes]
rs10013414	1.00[EUR][1000 genomes]
rs10013902	1.00[EUR][1000 genomes]
rs10017087	1.00[EUR][1000 genomes]
rs10019604	1.00[EUR][1000 genomes]
rs10021864	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10029008	1.00[EUR][1000 genomes]
rs10029089	1.00[EUR][1000 genomes]
rs10029265	1.00[EUR][1000 genomes]
rs16872671	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28414141	1.00[EUR][1000 genomes]
rs28426972	1.00[EUR][1000 genomes]
rs28490882	1.00[EUR][1000 genomes]
rs28501220	1.00[EUR][1000 genomes]
rs28518171	1.00[EUR][1000 genomes]
rs28521540	1.00[EUR][1000 genomes]
rs28542982	1.00[EUR][1000 genomes]
rs28591328	1.00[EUR][1000 genomes]
rs28645358	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28660699	1.00[EUR][1000 genomes]
rs28667991	1.00[EUR][1000 genomes]
rs28703830	1.00[EUR][1000 genomes]
rs28729399	1.00[EUR][1000 genomes]
rs28775576	1.00[EUR][1000 genomes]
rs28787887	1.00[EUR][1000 genomes]
rs28798753	1.00[EUR][1000 genomes]
rs28839846	1.00[EUR][1000 genomes]
rs28882371	1.00[EUR][1000 genomes]
rs34198330	1.00[EUR][1000 genomes]
rs6448148	1.00[EUR][1000 genomes]
rs6836362	1.00[EUR][1000 genomes]
rs6840912	1.00[EUR][1000 genomes]
rs6846776	1.00[EUR][1000 genomes]
rs73123531	1.00[EUR][1000 genomes]
rs73123532	1.00[EUR][1000 genomes]
rs73123536	1.00[EUR][1000 genomes]
rs7657782	1.00[EUR][1000 genomes]
rs7662891	1.00[EUR][1000 genomes]
rs7693660	1.00[EUR][1000 genomes]
rs9654097	1.00[EUR][1000 genomes]
rs980589	1.00[EUR][1000 genomes]
rs9992606	1.00[EUR][1000 genomes]
rs9993875	1.00[EUR][1000 genomes]
rs9995752	1.00[EUR][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:88 , 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	chr4:22437800-22465000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:22443400-22471200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:22443400-22472400	Weak transcription	Ovary	ovary
19	chr4:22443400-22473600	Weak transcription	Fetal Brain Female	brain
20	chr4:22443600-22470800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:22443600-22476200	Weak transcription	A549	lung
22	chr4:22443800-22474600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:22444000-22470800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr4:22447200-22467600	Weak transcription	Thymus	Thymus
25	chr4:22447200-22473800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr4:22447200-22475000	Weak transcription	NHLF	lung
27	chr4:22447800-22473400	Weak transcription	Brain Germinal Matrix	brain
28	chr4:22448000-22461400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:22448600-22472600	Weak transcription	Primary T cells from cord blood	blood
30	chr4:22450200-22471000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:22450200-22473800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr4:22450200-22473800	Weak transcription	NH-A	brain
33	chr4:22450400-22460200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr4:22450400-22461800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:22450400-22474800	Weak transcription	Adipose Nuclei	Adipose
36	chr4:22450400-22476000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:22450400-22484000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:22450400-22493200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:22450800-22464200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:22451400-22464000	Weak transcription	Fetal Stomach	stomach
41	chr4:22453400-22460800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr4:22453800-22460000	Weak transcription	Psoas Muscle	Psoas
43	chr4:22454400-22462200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr4:22455600-22474200	Weak transcription	Fetal Thymus	thymus
45	chr4:22456400-22459800	Weak transcription	HSMMtube	muscle
46	chr4:22456400-22461600	Weak transcription	HMEC	breast
47	chr4:22456400-22476200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr4:22456600-22462800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:22456600-22466200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr4:22456800-22459800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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