Variant report

Variant	rs28658027
Chromosome Location	chr4:74485664-74485665
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10011419	0.82[EUR][1000 genomes]
rs10019146	0.82[EUR][1000 genomes]
rs10019320	0.82[EUR][1000 genomes]
rs10020054	0.82[EUR][1000 genomes]
rs10021827	0.82[EUR][1000 genomes]
rs10029673	0.82[EUR][1000 genomes]
rs10518115	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1074085	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1247593	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1247651	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1247668	0.82[EUR][1000 genomes]
rs1247670	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1247671	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12503916	0.82[EUR][1000 genomes]
rs12505842	0.82[EUR][1000 genomes]
rs12506668	0.82[EUR][1000 genomes]
rs12506675	0.82[EUR][1000 genomes]
rs12507775	0.82[EUR][1000 genomes]
rs12508661	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13133747	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13144296	0.82[EUR][1000 genomes]
rs13144390	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1528915	0.81[EUR][1000 genomes]
rs1528916	0.83[EUR][1000 genomes]
rs1528917	0.83[EUR][1000 genomes]
rs1528918	0.83[EUR][1000 genomes]
rs16849628	0.82[EUR][1000 genomes]
rs16849629	0.82[EUR][1000 genomes]
rs16849651	0.82[EUR][1000 genomes]
rs16849656	0.82[EUR][1000 genomes]
rs16849659	0.82[EUR][1000 genomes]
rs16849675	0.83[EUR][1000 genomes]
rs16849677	0.83[EUR][1000 genomes]
rs17192413	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17805623	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2008288	0.82[EUR][1000 genomes]
rs28407399	0.82[EUR][1000 genomes]
rs28450939	0.82[EUR][1000 genomes]
rs28612539	0.82[EUR][1000 genomes]
rs28693538	0.82[EUR][1000 genomes]
rs34123018	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34773614	0.83[EUR][1000 genomes]
rs34832471	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34859660	0.83[EUR][1000 genomes]
rs4694626	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68145475	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6838329	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72649103	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7665563	0.83[EUR][1000 genomes]
rs7665972	0.83[EUR][1000 genomes]
rs7667019	0.83[EUR][1000 genomes]
rs7667185	0.83[EUR][1000 genomes]
rs7674913	0.82[EUR][1000 genomes]
rs7676850	0.82[EUR][1000 genomes]
rs7676870	0.82[EUR][1000 genomes]
rs7676884	0.82[EUR][1000 genomes]
rs7682201	0.82[EUR][1000 genomes]
rs7695792	0.83[EUR][1000 genomes]
rs7695946	0.83[EUR][1000 genomes]
rs7696502	0.82[EUR][1000 genomes]
rs9997572	0.84[ASN][1000 genomes]
rs9999939	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	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1008104	chr4:74468434-74621952	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74478600-74485800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr4:74481600-74486000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:74482000-74487000	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr4:74484400-74486400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr4:74484400-74486400	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr4:74484400-74486400	Active TSS	Rectal Mucosa Donor 31	rectum
7	chr4:74484400-74486800	Active TSS	Fetal Stomach	stomach
8	chr4:74484600-74486600	Active TSS	Fetal Intestine Large	intestine
9	chr4:74484800-74485800	Flanking Active TSS	HMEC	breast
10	chr4:74484800-74486200	Active TSS	Stomach Mucosa	stomach
11	chr4:74484800-74486600	Active TSS	Duodenum Mucosa	Duodenum
12	chr4:74484800-74486600	Active TSS	Fetal Intestine Small	intestine
13	chr4:74485000-74485800	Enhancers	Primary T cells from cord blood	blood
14	chr4:74485000-74486000	Active TSS	Rectal Smooth Muscle	rectum
15	chr4:74485000-74486200	Active TSS	Gastric	stomach
16	chr4:74485000-74486600	Active TSS	Colonic Mucosa	Colon
17	chr4:74485000-74486800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:74485000-74486800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:74485200-74485800	Enhancers	HepG2	liver
20	chr4:74485200-74486200	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr4:74485200-74486800	Active TSS	Fetal Kidney	kidney
22	chr4:74485400-74486200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
23	chr4:74485400-74486200	Active TSS	Pancreas	Pancrea
24	chr4:74485400-74486600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:74485400-74486600	Flanking Active TSS	Fetal Thymus	thymus
26	chr4:74485400-74486800	Active TSS	Thymus	Thymus
27	chr4:74485600-74485800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
28	chr4:74485600-74485800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
29	chr4:74485600-74485800	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr4:74485600-74485800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr4:74485600-74485800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:74485600-74485800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:74485600-74485800	Enhancers	Liver	Liver
34	chr4:74485600-74485800	Weak transcription	Placenta	Placenta
35	chr4:74485600-74485800	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
36	chr4:74485600-74485800	Bivalent/Poised TSS	GM12878-XiMat	blood
37	chr4:74485600-74485800	Enhancers	Hela-S3	cervix
38	chr4:74485600-74485800	Enhancers	K562	blood
39	chr4:74485600-74485800	Flanking Active TSS	NHEK	skin
40	chr4:74485600-74486000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:74485600-74486000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
42	chr4:74485600-74486000	Flanking Active TSS	A549	lung
43	chr4:74485600-74486200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:74485600-74486400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
45	chr4:74485600-74486400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
46	chr4:74485600-74486400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
47	chr4:74485600-74486600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:74485600-74486600	Active TSS	Esophagus	oesophagus
49	chr4:74485600-74486800	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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