Variant report

Variant	rs58968032
Chromosome Location	chr4:26886296-26886297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10029307	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11729927	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11730235	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11734308	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11737218	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11943948	0.92[ASN][1000 genomes]
rs12641261	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12644073	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12646473	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12650172	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13116341	0.86[ASN][1000 genomes]
rs13138942	0.95[ASN][1000 genomes]
rs13139464	0.88[ASN][1000 genomes]
rs28497454	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28520489	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34996346	0.94[ASN][1000 genomes]
rs3792685	0.84[ASN][1000 genomes]
rs3924178	0.86[ASN][1000 genomes]
rs4274829	0.92[ASN][1000 genomes]
rs4407490	0.85[ASN][1000 genomes]
rs4505809	0.95[ASN][1000 genomes]
rs4519790	0.92[ASN][1000 genomes]
rs4532223	0.92[ASN][1000 genomes]
rs4557250	0.92[ASN][1000 genomes]
rs4557251	0.91[ASN][1000 genomes]
rs57663175	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57686546	0.91[ASN][1000 genomes]
rs58075729	0.85[ASN][1000 genomes]
rs60890366	0.89[ASN][1000 genomes]
rs61047003	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62302532	0.87[ASN][1000 genomes]
rs62302533	0.87[ASN][1000 genomes]
rs62302535	0.86[ASN][1000 genomes]
rs6448479	0.93[ASN][1000 genomes]
rs6448484	0.95[ASN][1000 genomes]
rs6448488	0.87[ASN][1000 genomes]
rs6815719	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6833053	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6833895	0.93[ASN][1000 genomes]
rs6835631	0.89[ASN][1000 genomes]
rs6844153	0.89[ASN][1000 genomes]
rs6853032	0.94[ASN][1000 genomes]
rs73116683	0.87[ASN][1000 genomes]
rs73811400	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73813220	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7655686	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9790789	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58968032	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26864400-26886600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr4:26875600-26904600	Weak transcription	Brain Anterior Caudate	brain
3	chr4:26875800-26888200	Weak transcription	Adipose Nuclei	Adipose
4	chr4:26880600-26902400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:26880600-26921600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:26881800-26886800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:26881800-26896200	Weak transcription	HMEC	breast
8	chr4:26882000-26887800	Weak transcription	Stomach Mucosa	stomach
9	chr4:26882000-26897000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:26882200-26889000	Weak transcription	K562	blood
11	chr4:26883400-26892800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr4:26883600-26887200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:26884200-26886400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr4:26884200-26886400	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:26884600-26888000	Weak transcription	Spleen	Spleen
16	chr4:26885000-26887000	Enhancers	Fetal Heart	heart
17	chr4:26885000-26887600	Enhancers	Primary hematopoietic stem cells	blood
18	chr4:26885000-26887600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:26885200-26886600	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr4:26885200-26888600	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr4:26885400-26886600	Enhancers	Small Intestine	intestine
22	chr4:26885400-26887000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:26885400-26887000	Enhancers	Duodenum Mucosa	Duodenum
24	chr4:26885400-26887200	Flanking Active TSS	GM12878-XiMat	blood
25	chr4:26885400-26887400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr4:26885400-26887400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr4:26885400-26889200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr4:26885400-26889200	Flanking Active TSS	Dnd41	blood
29	chr4:26885600-26886400	Enhancers	H9 Cell Line	embryonic stem cell
30	chr4:26885600-26886400	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr4:26885600-26886400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr4:26885600-26886600	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr4:26885600-26886600	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr4:26885600-26886600	Enhancers	Brain Angular Gyrus	brain
35	chr4:26885600-26886600	Enhancers	Fetal Muscle Leg	muscle
36	chr4:26885600-26886600	Enhancers	Thymus	Thymus
37	chr4:26885600-26887000	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr4:26885600-26887400	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr4:26885600-26887400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr4:26885600-26887400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr4:26885600-26887400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr4:26885600-26887400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr4:26885600-26887600	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr4:26885600-26887800	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr4:26885800-26886400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr4:26885800-26886400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr4:26885800-26886400	Active TSS	Rectal Smooth Muscle	rectum
48	chr4:26885800-26886400	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr4:26885800-26886600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr4:26885800-26886600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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