Variant report

Variant	rs13129075
Chromosome Location	chr4:26942749-26942750
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:26935465..26937974-chr4:26941266..26944135,2	K562	blood:
2	chr4:26941693..26944316-chr4:26946702..26948605,2	K562	blood:
3	chr4:26935465..26938431-chr4:26942635..26945108,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10002654	0.82[EUR][1000 genomes]
rs10470822	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10939142	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10939144	0.82[EUR][1000 genomes]
rs12644232	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17555311	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28454570	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28704572	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4259045	0.80[ASN][1000 genomes]
rs4519791	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4575981	0.80[ASN][1000 genomes]
rs4692131	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6448482	0.80[ASN][1000 genomes]
rs6448483	0.80[ASN][1000 genomes]
rs6448485	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6448487	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6831605	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6847438	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs725981	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7658174	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7666651	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7672936	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7692953	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9998368	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv966490	chr4:26940200-26946323	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13129075	STIM2	cis	Whole Blood	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26911600-26965800	Weak transcription	HMEC	breast
2	chr4:26923200-26965800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:26923200-26977200	Weak transcription	Thymus	Thymus
4	chr4:26923400-26954400	Weak transcription	HSMM	muscle
5	chr4:26923400-26960600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:26923800-26943800	Weak transcription	Fetal Lung	lung
7	chr4:26924400-26955200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:26936000-26944600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr4:26938000-26945000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr4:26938600-26969000	Weak transcription	Gastric	stomach
11	chr4:26938800-26945000	Weak transcription	Psoas Muscle	Psoas
12	chr4:26938800-26965600	Weak transcription	NHLF	lung
13	chr4:26939000-26954000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr4:26939200-26948000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:26939200-26949200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:26939200-26969000	Weak transcription	Pancreas	Pancrea
17	chr4:26939600-26943800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:26940200-26942800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr4:26940200-26943200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr4:26940200-26944600	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr4:26940200-26945200	Enhancers	Ovary	ovary
22	chr4:26940400-26945600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr4:26940400-26947800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr4:26940600-26942800	Enhancers	Primary B cells from peripheral blood	blood
25	chr4:26940600-26944600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:26940800-26942800	Enhancers	Brain Substantia Nigra	brain
27	chr4:26940800-26943000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr4:26940800-26944200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:26941200-26943000	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr4:26941400-26942800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr4:26941400-26942800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr4:26941400-26942800	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr4:26941400-26942800	Enhancers	Brain Hippocampus Middle	brain
34	chr4:26941400-26943000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr4:26941400-26944200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr4:26941400-26945400	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr4:26941800-26942800	Enhancers	Fetal Stomach	stomach
38	chr4:26942000-26942800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr4:26942000-26942800	Enhancers	Stomach Mucosa	stomach
40	chr4:26942000-26943000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:26942000-26943000	Enhancers	Primary B cells from cord blood	blood
42	chr4:26942000-26961000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr4:26942200-26942800	Enhancers	Brain Anterior Caudate	brain
44	chr4:26942200-26943200	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr4:26942200-26943800	Weak transcription	K562	blood
46	chr4:26942400-26942800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:26942400-26942800	Enhancers	Brain Angular Gyrus	brain
48	chr4:26942400-26942800	Enhancers	Fetal Brain Male	brain
49	chr4:26942400-26945200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr4:26942600-26942800	Enhancers	H9 Cell Line	embryonic stem cell

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