Variant report

Variant	rs10939146
Chromosome Location	chr4:26980021-26980022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12642922	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16878655	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16878719	0.80[AMR][1000 genomes]
rs16878720	0.83[AMR][1000 genomes]
rs62299310	0.81[AMR][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
rs10939146	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26950000-26980200	Weak transcription	Spleen	Spleen
2	chr4:26961800-26980200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr4:26961800-26994000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr4:26963600-26994200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:26966600-26986400	Weak transcription	HSMM	muscle
6	chr4:26966600-26989000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:26966600-26994600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:26966800-26985200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:26966800-26986400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr4:26967600-26986400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:26975800-26980400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:26975800-27003200	Weak transcription	Aorta	Aorta
13	chr4:26977200-26980800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr4:26977800-26988600	Weak transcription	Fetal Thymus	thymus
15	chr4:26978000-26980200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:26978000-26987400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:26978000-26994600	Weak transcription	Fetal Stomach	stomach
18	chr4:26978200-26984600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:26978400-27019200	Weak transcription	Fetal Intestine Small	intestine
20	chr4:26978600-26980600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr4:26978800-26980600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr4:26978800-26980600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr4:26978800-26988600	Weak transcription	Fetal Muscle Leg	muscle
24	chr4:26979000-26981200	Enhancers	Primary T cells from cord blood	blood
25	chr4:26979200-26980600	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr4:26979400-26980400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr4:26979400-26980400	Enhancers	Lung	lung
28	chr4:26979400-26980400	Enhancers	Ovary	ovary
29	chr4:26979400-26980400	Enhancers	Pancreas	Pancrea
30	chr4:26979400-26980600	Enhancers	Psoas Muscle	Psoas
31	chr4:26979400-26980800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:26979400-26981200	Enhancers	Primary B cells from peripheral blood	blood
33	chr4:26979600-26988600	Weak transcription	Thymus	Thymus
34	chr4:26980000-26980400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:26980000-26980600	Enhancers	Primary T cells fromperipheralblood	blood
36	chr4:26980000-26981200	Enhancers	GM12878-XiMat	blood
37	chr4:26980000-26981400	Enhancers	Primary B cells from cord blood	blood

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