Variant report

Variant	rs725981
Chromosome Location	chr4:26961239-26961240
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10470822	0.81[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs10939142	0.82[AMR][1000 genomes]
rs10939144	0.85[CEU][hapmap];0.87[MEX][hapmap];0.83[EUR][1000 genomes]
rs12644232	0.88[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13129075	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17555311	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28454570	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28704572	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4519791	0.92[ASW][hapmap];0.81[CEU][hapmap];0.87[MEX][hapmap]
rs4692131	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4692137	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs6448478	0.89[JPT][hapmap]
rs6448485	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs6448487	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]
rs6822297	0.82[CEU][hapmap]
rs6831605	0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6847438	0.89[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7658174	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7666651	0.84[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7672936	0.92[ASW][hapmap];0.81[CEU][hapmap];0.82[MEX][hapmap]
rs7692953	0.85[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9998368	1.00[ASW][hapmap];0.89[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][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	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
3	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
4	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
rs725981	STIM2	cis	Whole Blood	GTEx

Chromatin state (count:76 , 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	chr4:26938600-26969000	Weak transcription	Gastric	stomach
5	chr4:26938800-26965600	Weak transcription	NHLF	lung
6	chr4:26939200-26969000	Weak transcription	Pancreas	Pancrea
7	chr4:26944400-26965600	Weak transcription	Brain Anterior Caudate	brain
8	chr4:26949200-26965600	Weak transcription	NH-A	brain
9	chr4:26949400-26963400	Weak transcription	Lung	lung
10	chr4:26950000-26980200	Weak transcription	Spleen	Spleen
11	chr4:26950200-26979400	Weak transcription	Ovary	ovary
12	chr4:26952600-26965600	Weak transcription	Psoas Muscle	Psoas
13	chr4:26952800-26963400	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:26953200-26961400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:26955400-26962600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:26955400-26963600	Weak transcription	HSMMtube	muscle
17	chr4:26955600-26963000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:26955600-26965600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:26955600-26965600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:26955600-26965600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:26955600-26965600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr4:26955600-26965600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr4:26955600-26965600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:26955600-26966400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:26956000-26966400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr4:26957400-26961400	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:26957400-26961400	Weak transcription	Brain Substantia Nigra	brain
28	chr4:26957400-26961800	Weak transcription	Colon Smooth Muscle	Colon
29	chr4:26957400-26964600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:26957400-26966600	Weak transcription	Small Intestine	intestine
31	chr4:26957600-26964200	Weak transcription	Fetal Lung	lung
32	chr4:26958000-26965600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:26958600-26965600	Weak transcription	Brain Angular Gyrus	brain
34	chr4:26958600-26965800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:26959000-26961800	Strong transcription	Primary B cells from cord blood	blood
36	chr4:26959000-26966400	Weak transcription	Liver	Liver
37	chr4:26959200-26961800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:26959200-26962000	Weak transcription	Placenta	Placenta
39	chr4:26959200-26963400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr4:26959200-26977600	Weak transcription	Fetal Thymus	thymus
41	chr4:26959400-26964000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr4:26959600-26961800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr4:26959600-26961800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr4:26959800-26961800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
45	chr4:26959800-26963400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr4:26960000-26961800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr4:26960200-26961600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:26960400-26961400	Enhancers	GM12878-XiMat	blood
49	chr4:26960400-26961600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:26960400-26961600	Genic enhancers	Primary T cells from cord blood	blood

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