Variant report

Variant	rs28520489
Chromosome Location	chr4:26897704-26897705
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10029307	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11729927	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11730235	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11734308	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11737218	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11943948	0.86[ASN][1000 genomes]
rs12641261	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12644073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12646473	0.89[ASN][1000 genomes]
rs12650172	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13138942	0.87[ASN][1000 genomes]
rs13139464	0.82[ASN][1000 genomes]
rs28497454	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34996346	0.87[ASN][1000 genomes]
rs3792685	0.85[ASN][1000 genomes]
rs4274829	0.86[ASN][1000 genomes]
rs4505809	0.87[ASN][1000 genomes]
rs4519790	0.86[ASN][1000 genomes]
rs4532223	0.86[ASN][1000 genomes]
rs4557250	0.86[ASN][1000 genomes]
rs4557251	0.85[ASN][1000 genomes]
rs57663175	0.93[ASN][1000 genomes]
rs57686546	0.92[ASN][1000 genomes]
rs58968032	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60890366	0.89[ASN][1000 genomes]
rs61047003	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62302532	0.88[ASN][1000 genomes]
rs62302533	0.88[ASN][1000 genomes]
rs62302535	0.86[ASN][1000 genomes]
rs6448479	0.87[ASN][1000 genomes]
rs6448484	0.87[ASN][1000 genomes]
rs6448488	0.88[ASN][1000 genomes]
rs6815719	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6833053	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6833895	0.87[ASN][1000 genomes]
rs6835631	0.89[ASN][1000 genomes]
rs6844153	0.89[ASN][1000 genomes]
rs6853032	0.87[ASN][1000 genomes]
rs73116683	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73811400	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73813220	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7655686	0.94[ASN][1000 genomes]
rs9790789	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470021	chr4:26721578-27067027	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1001306	chr4:26821511-26955344	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv461312	chr4:26844674-27078376	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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
4	nsv593872	chr4:26844674-27078376	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1000568	chr4:26886920-27049554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28520489	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26875600-26904600	Weak transcription	Brain Anterior Caudate	brain
2	chr4:26880600-26902400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:26880600-26921600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr4:26885800-26903600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:26886600-26899400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr4:26886600-26921600	Weak transcription	Fetal Muscle Leg	muscle
7	chr4:26888400-26901600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:26888600-26899400	Weak transcription	Spleen	Spleen
9	chr4:26889800-26901800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:26889800-26906000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:26891800-26899400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr4:26893400-26901600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:26893600-26901800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:26894600-26903400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:26894800-26899400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr4:26894800-26899600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr4:26894800-26899800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:26894800-26899800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr4:26894800-26901600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:26895200-26898800	Enhancers	NHEK	skin
21	chr4:26895200-26901200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:26895400-26898800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr4:26895400-26899400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr4:26895400-26899600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:26895400-26899600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr4:26895400-26900000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr4:26895400-26901200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr4:26895600-26898000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:26895800-26899400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr4:26896200-26897800	Enhancers	HMEC	breast
31	chr4:26896600-26898400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:26896800-26898200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:26897000-26899000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:26897200-26897800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:26897200-26897800	Enhancers	Fetal Heart	heart
36	chr4:26897200-26898600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr4:26897400-26898000	Strong transcription	Primary B cells from cord blood	blood
38	chr4:26897400-26898000	Strong transcription	Primary T cells from cord blood	blood
39	chr4:26897600-26897800	Enhancers	Left Ventricle	heart
40	chr4:26897600-26897800	Enhancers	Pancreas	Pancrea
41	chr4:26897600-26898000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:26897600-26898000	Enhancers	Ovary	ovary
43	chr4:26897600-26898600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:26897600-26899000	Enhancers	NHLF	lung

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