Variant report

Variant	rs28726245
Chromosome Location	chr4:22450122-22450123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:22449726..22452368-chr4:22458347..22461364,3	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10003859	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10003883	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10014897	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10022239	0.81[CEU][hapmap]
rs10025779	0.80[CEU][hapmap]
rs1020917	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs10516411	0.85[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs13109198	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs13110697	0.82[JPT][hapmap]
rs13129189	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13139516	0.88[JPT][hapmap]
rs13145061	0.85[ASN][1000 genomes]
rs1564138	0.84[CEU][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs1564139	0.84[CEU][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs16872664	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16872676	0.81[EUR][1000 genomes]
rs16872682	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs16872686	0.92[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap]
rs2126633	0.92[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap]
rs28386903	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28437151	0.86[ASN][1000 genomes]
rs28736882	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35852147	0.87[ASN][1000 genomes]
rs36111920	0.90[ASN][1000 genomes]
rs4583743	0.91[CEU][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs4697300	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4697301	0.90[ASN][1000 genomes]
rs4697304	0.89[ASN][1000 genomes]
rs59022936	0.90[ASN][1000 genomes]
rs60379399	0.90[ASN][1000 genomes]
rs71182940	0.87[EUR][1000 genomes]
rs71608917	0.84[ASN][1000 genomes]
rs7657579	0.91[CEU][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs7688074	0.82[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:89 , 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	chr4:22390600-22456200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:22390600-22459800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:22393600-22459800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:22393800-22453000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:22400800-22461800	Weak transcription	Gastric	stomach
9	chr4:22419200-22476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:22419400-22465800	Weak transcription	HUVEC	blood vessel
11	chr4:22420600-22488000	Weak transcription	Aorta	Aorta
12	chr4:22422000-22453400	Weak transcription	Esophagus	oesophagus
13	chr4:22424400-22457800	Weak transcription	Dnd41	blood
14	chr4:22426000-22461800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:22428600-22460600	Weak transcription	Placenta	Placenta
16	chr4:22429400-22457800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr4:22430600-22456000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:22432400-22451400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:22432400-22460400	Weak transcription	Small Intestine	intestine
20	chr4:22433800-22479200	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:22434000-22461200	Weak transcription	Brain Anterior Caudate	brain
22	chr4:22434800-22456000	Weak transcription	Brain Substantia Nigra	brain
23	chr4:22436800-22456200	Weak transcription	NHEK	skin
24	chr4:22437400-22476400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:22437800-22453400	Weak transcription	Fetal Heart	heart
26	chr4:22437800-22459600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:22437800-22465000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr4:22439200-22451800	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:22439200-22458000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:22439600-22450600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr4:22441800-22452000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:22442400-22450200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:22442400-22450200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:22443000-22453000	Weak transcription	Psoas Muscle	Psoas
35	chr4:22443400-22471200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:22443400-22472400	Weak transcription	Ovary	ovary
37	chr4:22443400-22473600	Weak transcription	Fetal Brain Female	brain
38	chr4:22443600-22470800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr4:22443600-22476200	Weak transcription	A549	lung
40	chr4:22443800-22474600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:22444000-22470800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr4:22445000-22452800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:22445800-22450400	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr4:22445800-22456600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:22446400-22450200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:22446600-22450400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:22446600-22450400	Strong transcription	HSMMtube	muscle
48	chr4:22446800-22450200	Strong transcription	Primary hematopoietic stem cells	blood
49	chr4:22446800-22450200	Strong transcription	HMEC	breast
50	chr4:22447000-22455600	Weak transcription	Pancreas	Pancrea

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