Variant report

Variant	rs28562313
Chromosome Location	chr4:74464995-74464996
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10000698	1.00[AMR][1000 genomes]
rs10011419	0.81[AFR][1000 genomes]
rs10011693	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10015321	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10015884	1.00[AMR][1000 genomes]
rs10019146	0.81[AFR][1000 genomes]
rs10019320	0.81[AFR][1000 genomes]
rs10020054	0.80[AFR][1000 genomes]
rs10029673	0.80[AFR][1000 genomes]
rs10032183	1.00[AMR][1000 genomes]
rs10034509	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10049835	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1105321	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12331864	1.00[AMR][1000 genomes]
rs12503916	0.80[AFR][1000 genomes]
rs12505842	0.80[AFR][1000 genomes]
rs12506668	0.80[AFR][1000 genomes]
rs12506675	0.80[AFR][1000 genomes]
rs12507775	0.80[AFR][1000 genomes]
rs13144296	0.81[AFR][1000 genomes]
rs1528922	0.83[AMR][1000 genomes]
rs16849498	1.00[AMR][1000 genomes]
rs16849628	0.80[AFR][1000 genomes]
rs16849629	0.80[AFR][1000 genomes]
rs16849651	0.80[AFR][1000 genomes]
rs16849656	0.80[AFR][1000 genomes]
rs16849675	0.80[AFR][1000 genomes]
rs2008288	0.80[AFR][1000 genomes]
rs2367164	1.00[AMR][1000 genomes]
rs28407399	0.80[AFR][1000 genomes]
rs28450939	0.80[AFR][1000 genomes]
rs28533985	1.00[AMR][1000 genomes]
rs28570600	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28649464	1.00[AMR][1000 genomes]
rs28651748	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28693538	0.80[AFR][1000 genomes]
rs28755465	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34859660	0.81[AFR][1000 genomes]
rs6831133	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7356389	1.00[AMR][1000 genomes]
rs7665563	0.81[AFR][1000 genomes]
rs7665972	0.81[AFR][1000 genomes]
rs7667019	0.81[AFR][1000 genomes]
rs7667185	0.81[AFR][1000 genomes]
rs7674913	0.80[AFR][1000 genomes]
rs7676850	0.80[AFR][1000 genomes]
rs7676870	0.80[AFR][1000 genomes]
rs7676884	0.80[AFR][1000 genomes]
rs7682201	0.80[AFR][1000 genomes]
rs7695792	0.81[AFR][1000 genomes]
rs7695946	0.81[AFR][1000 genomes]
rs7696502	0.81[AFR][1000 genomes]
rs9291186	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9995788	1.00[AMR][1000 genomes]
rs9999939	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74440200-74472600	Weak transcription	Gastric	stomach
2	chr4:74449000-74470200	Weak transcription	Primary T cells from cord blood	blood
3	chr4:74456400-74472200	Weak transcription	Colonic Mucosa	Colon
4	chr4:74463600-74470400	Enhancers	Fetal Intestine Large	intestine
5	chr4:74463800-74474200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:74464200-74465800	Enhancers	Hela-S3	cervix
7	chr4:74464200-74466000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:74464200-74476400	Enhancers	Stomach Mucosa	stomach
9	chr4:74464200-74477200	Enhancers	Fetal Intestine Small	intestine
10	chr4:74464400-74465400	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr4:74464400-74465400	Flanking Active TSS	HepG2	liver
12	chr4:74464400-74465600	Enhancers	GM12878-XiMat	blood
13	chr4:74464400-74465800	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr4:74464600-74465000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:74464600-74465000	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr4:74464600-74465000	Flanking Active TSS	Thymus	Thymus
17	chr4:74464600-74465000	Flanking Active TSS	HMEC	breast
18	chr4:74464600-74465000	Flanking Active TSS	NHEK	skin
19	chr4:74464600-74465200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:74464600-74465200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:74464600-74465400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:74464600-74465400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:74464600-74465400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr4:74464600-74465400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:74464600-74465600	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr4:74464600-74465600	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr4:74464600-74465600	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr4:74464600-74465600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:74464600-74465600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:74464600-74465800	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr4:74464600-74465800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:74464600-74465800	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr4:74464600-74465800	Enhancers	NHLF	lung
34	chr4:74464600-74466000	Enhancers	Muscle Satellite Cultured Cells	--
35	chr4:74464600-74466000	Flanking Active TSS	A549	lung
36	chr4:74464600-74466400	Enhancers	HSMM	muscle
37	chr4:74464600-74467000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:74464800-74465000	Enhancers	Primary B cells from peripheral blood	blood
39	chr4:74464800-74465000	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr4:74464800-74465200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:74464800-74465200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr4:74464800-74465200	Flanking Active TSS	K562	blood
43	chr4:74464800-74465200	Enhancers	NHDF-Ad	bronchial
44	chr4:74464800-74465400	Enhancers	H1 Cell Line	embryonic stem cell
45	chr4:74464800-74465400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:74464800-74465400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr4:74464800-74465400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:74464800-74465400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:74464800-74465400	Enhancers	Esophagus	oesophagus
50	chr4:74464800-74465400	Enhancers	Sigmoid Colon	Sigmoid Colon

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