Variant report

Variant	rs6448485
Chromosome Location	chr4:26875266-26875267
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10006403	0.81[CEU][hapmap]
rs10023256	0.85[CEU][hapmap]
rs10470822	0.93[CEU][hapmap]
rs10939144	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs12331333	0.85[CEU][hapmap]
rs12644232	0.82[CEU][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13129075	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13434709	0.86[CEU][hapmap]
rs17555311	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs28454570	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28704572	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3924177	0.94[ASN][1000 genomes]
rs4259045	0.95[ASN][1000 genomes]
rs4376128	0.94[ASN][1000 genomes]
rs4519791	0.92[CEU][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4575981	0.95[ASN][1000 genomes]
rs4692131	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4692132	0.85[CEU][hapmap]
rs4692137	0.96[CEU][hapmap]
rs6448478	0.88[ASN][1000 genomes]
rs6448480	0.87[ASN][1000 genomes]
rs6448481	0.89[ASN][1000 genomes]
rs6448482	0.95[ASN][1000 genomes]
rs6448483	0.95[ASN][1000 genomes]
rs6448487	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6822297	0.92[CEU][hapmap]
rs6830424	0.90[ASN][1000 genomes]
rs6831605	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6847438	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs724624	0.84[CEU][hapmap]
rs725981	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7658174	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7666651	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7672936	0.92[CEU][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7692953	0.96[CEU][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9654110	0.85[CEU][hapmap]
rs9998368	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6448485	STIM2	cis	Whole Blood	GTEx
rs6448485	STIM2	cis	uninvolved skin	skin_eQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26863800-26875400	Weak transcription	Lung	lung
2	chr4:26864200-26876800	Weak transcription	Colonic Mucosa	Colon
3	chr4:26864200-26877200	Weak transcription	Aorta	Aorta
4	chr4:26864400-26886600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:26864600-26885600	Weak transcription	Thymus	Thymus
6	chr4:26865600-26876000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr4:26866000-26880400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:26866000-26881800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:26867200-26879000	Weak transcription	Fetal Intestine Small	intestine
10	chr4:26867200-26880000	Weak transcription	Fetal Intestine Large	intestine
11	chr4:26867200-26884200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:26869400-26876200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:26869600-26876000	Enhancers	Primary T cells from cord blood	blood
14	chr4:26869800-26875400	Weak transcription	Pancreas	Pancrea
15	chr4:26869800-26877000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr4:26869800-26886000	Weak transcription	Fetal Stomach	stomach
17	chr4:26870000-26876400	Weak transcription	Brain Substantia Nigra	brain
18	chr4:26870000-26879400	Weak transcription	NHLF	lung
19	chr4:26870000-26879600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:26870400-26875800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:26870600-26881800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr4:26870800-26879200	Weak transcription	Small Intestine	intestine
23	chr4:26870800-26880800	Weak transcription	Stomach Mucosa	stomach
24	chr4:26871000-26875400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr4:26871000-26875400	Weak transcription	Psoas Muscle	Psoas
26	chr4:26871400-26876800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr4:26871600-26876800	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr4:26872200-26876000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:26872800-26877400	Weak transcription	HSMMtube	muscle
30	chr4:26873000-26886200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr4:26873200-26875800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:26873400-26875600	Enhancers	Primary B cells from cord blood	blood
33	chr4:26873400-26877800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr4:26873400-26883600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:26873600-26875400	Weak transcription	Ovary	ovary
36	chr4:26873600-26875800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:26873600-26875800	Weak transcription	Fetal Lung	lung
38	chr4:26873600-26876400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr4:26873600-26879200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:26873600-26880000	Weak transcription	NHEK	skin
41	chr4:26873800-26876200	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr4:26873800-26880000	Weak transcription	HMEC	breast
43	chr4:26873800-26881200	Weak transcription	Fetal Heart	heart
44	chr4:26873800-26881400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:26874000-26875600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:26874000-26875800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:26874200-26876000	Enhancers	Primary B cells from peripheral blood	blood
48	chr4:26874400-26875800	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr4:26874400-26875800	Enhancers	GM12878-XiMat	blood
50	chr4:26874400-26876000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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