Variant report

Variant	rs6448487
Chromosome Location	chr4:26945527-26945528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10006403	0.80[CEU][hapmap]
rs10023256	0.85[CEU][hapmap]
rs10470822	0.92[CEU][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10939142	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10939144	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs12331333	0.84[CEU][hapmap]
rs12644232	0.81[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13129075	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13434709	0.85[CEU][hapmap]
rs17555311	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28454570	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28704572	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4519791	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs4692131	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4692132	0.85[CEU][hapmap]
rs4692137	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs6448478	0.95[JPT][hapmap]
rs6448485	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6822297	0.92[CEU][hapmap]
rs6831605	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6847438	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs724624	0.84[CEU][hapmap]
rs725981	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7658174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7666651	0.84[CHB][hapmap];0.93[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7672936	0.92[CEU][hapmap]
rs7692953	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9654110	0.85[CEU][hapmap]
rs9998368	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
7	esv1000535	chr4:26944042-26955394	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv1812289	chr4:26945149-26957436	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1808465	chr4:26945149-26957489	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6448487	STIM2	cis	Whole Blood	GTEx
rs6448487	STIM2	cis	uninvolved skin	skin_eQTL

Chromatin state (count:36 , 50 per page) page: 1

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	chr4:26924400-26955200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:26938600-26969000	Weak transcription	Gastric	stomach
8	chr4:26938800-26965600	Weak transcription	NHLF	lung
9	chr4:26939000-26954000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr4:26939200-26948000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:26939200-26949200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr4:26939200-26969000	Weak transcription	Pancreas	Pancrea
13	chr4:26940400-26945600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr4:26940400-26947800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr4:26942000-26961000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:26942600-26950400	Weak transcription	Left Ventricle	heart
17	chr4:26942800-26947000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr4:26942800-26948000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:26943000-26948000	Weak transcription	Primary B cells from cord blood	blood
20	chr4:26943200-26955000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr4:26944000-26950600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr4:26944000-26952000	Weak transcription	Primary T cells from cord blood	blood
23	chr4:26944200-26949800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:26944200-26952000	Weak transcription	Fetal Stomach	stomach
25	chr4:26944200-26952800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:26944400-26965600	Weak transcription	Brain Anterior Caudate	brain
27	chr4:26944600-26948000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr4:26945000-26945600	Enhancers	Brain Substantia Nigra	brain
29	chr4:26945000-26945800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr4:26945200-26949200	Weak transcription	Ovary	ovary
31	chr4:26945200-26949200	Weak transcription	Psoas Muscle	Psoas
32	chr4:26945200-26952000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr4:26945200-26954600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:26945200-26956800	Weak transcription	Brain Angular Gyrus	brain
35	chr4:26945400-26945600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:26945400-26954600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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