Variant report

Variant	rs28925939
Chromosome Location	chr4:144379874-144379875
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10000941	0.83[ASN][1000 genomes]
rs10008867	0.83[ASN][1000 genomes]
rs10084783	0.83[ASN][1000 genomes]
rs11725272	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735967	0.83[ASN][1000 genomes]
rs11933502	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11936966	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11945261	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12512923	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13112122	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13112412	0.82[EUR][1000 genomes]
rs13114896	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13128753	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1397529	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17017801	0.85[EUR][1000 genomes]
rs1995931	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28776014	0.86[EUR][1000 genomes]
rs28924075	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28925907	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28925924	0.84[EUR][1000 genomes]
rs28925926	0.86[EUR][1000 genomes]
rs35152330	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3795246	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4690785	0.82[AMR][1000 genomes]
rs59727559	0.86[EUR][1000 genomes]
rs6833624	0.86[EUR][1000 genomes]
rs6837153	0.83[ASN][1000 genomes]
rs7696619	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7698825	0.83[EUR][1000 genomes]
rs9684453	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9685389	0.85[EUR][1000 genomes]
rs9995486	0.83[ASN][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	esv2757960	chr4:144348293-145131592	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	esv2759288	chr4:144348293-145131592	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1019980	chr4:144350575-144399936	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144327800-144388200	Weak transcription	HepG2	liver
2	chr4:144336400-144392200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:144339400-144394600	Weak transcription	Colonic Mucosa	Colon
4	chr4:144342000-144382000	Weak transcription	Fetal Kidney	kidney
5	chr4:144347000-144382600	Weak transcription	Gastric	stomach
6	chr4:144352400-144382200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:144353200-144398600	Weak transcription	Brain Germinal Matrix	brain
8	chr4:144353600-144400000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:144355200-144382400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:144355600-144388200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr4:144358200-144387000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:144358400-144384400	Weak transcription	HSMM	muscle
13	chr4:144359800-144382600	Weak transcription	Esophagus	oesophagus
14	chr4:144360000-144380600	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:144360000-144388400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:144360200-144380400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr4:144360200-144382400	Weak transcription	Aorta	Aorta
18	chr4:144360200-144383800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:144360200-144387200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:144360200-144399000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:144361600-144390400	Weak transcription	K562	blood
22	chr4:144361800-144381600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:144362000-144380200	Weak transcription	Adipose Nuclei	Adipose
24	chr4:144362000-144380600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:144362000-144380600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:144362000-144381400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:144362600-144380800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:144363200-144380600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:144363200-144381800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr4:144363200-144395400	Weak transcription	Spleen	Spleen
31	chr4:144363200-144398600	Weak transcription	Lung	lung
32	chr4:144363400-144380600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:144363600-144381400	Weak transcription	Ovary	ovary
34	chr4:144363800-144380600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:144363800-144380600	Weak transcription	Placenta	Placenta
36	chr4:144365400-144380600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:144365600-144382400	Weak transcription	Brain Anterior Caudate	brain
38	chr4:144365600-144398400	Weak transcription	NHLF	lung
39	chr4:144366200-144384400	Weak transcription	HUVEC	blood vessel
40	chr4:144366200-144394400	Weak transcription	Psoas Muscle	Psoas
41	chr4:144372600-144381400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr4:144372800-144382200	Weak transcription	Fetal Intestine Small	intestine
43	chr4:144373200-144399000	Weak transcription	Fetal Brain Male	brain
44	chr4:144373400-144380200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr4:144373400-144381800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr4:144375000-144390400	Weak transcription	Stomach Mucosa	stomach
47	chr4:144376000-144382600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr4:144376000-144383800	Weak transcription	Right Ventricle	heart
49	chr4:144376000-144391400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr4:144376000-144392800	Weak transcription	H1 Cell Line	embryonic stem cell

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