Variant report

Variant	rs10939141
Chromosome Location	chr4:26921467-26921468
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10007132	0.90[CEU][hapmap]
rs10022599	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10030655	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10213674	0.85[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap]
rs10433805	0.86[CEU][hapmap]
rs10470823	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10939140	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10939143	0.81[EUR][1000 genomes]
rs1122045	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11722221	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs11722323	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs11727649	0.81[CEU][hapmap]
rs12331378	0.90[CEU][hapmap]
rs12505133	0.81[CEU][hapmap]
rs13114545	0.86[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap]
rs13115054	0.85[CEU][hapmap]
rs13127603	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13147585	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13152367	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28391037	0.81[EUR][1000 genomes]
rs4586918	0.81[CEU][hapmap]
rs4692136	0.90[CEU][hapmap]
rs6830016	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6830950	0.86[CEU][hapmap]
rs7655631	0.95[CEU][hapmap]
rs7667007	0.80[CEU][hapmap]
rs7693687	0.86[CEU][hapmap]
rs7695335	0.85[CEU][hapmap]
rs9998009	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10939141	STIM2	cis	multi-tissue	Pritchard
rs10939141	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26880600-26921600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:26886600-26921600	Weak transcription	Fetal Muscle Leg	muscle
3	chr4:26907200-26937800	Weak transcription	Stomach Mucosa	stomach
4	chr4:26909600-26923000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:26910000-26926600	Weak transcription	Fetal Stomach	stomach
6	chr4:26910200-26925800	Weak transcription	NHEK	skin
7	chr4:26910800-26921800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:26911600-26965800	Weak transcription	HMEC	breast
9	chr4:26912600-26921600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:26914000-26923000	Weak transcription	Aorta	Aorta
11	chr4:26914200-26924200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:26914600-26921600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr4:26914600-26921600	Weak transcription	Fetal Intestine Large	intestine
14	chr4:26914600-26921600	Weak transcription	Thymus	Thymus
15	chr4:26914600-26921800	Weak transcription	Fetal Brain Male	brain
16	chr4:26914600-26924800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:26914600-26936800	Weak transcription	Small Intestine	intestine
18	chr4:26914800-26921600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:26914800-26921600	Weak transcription	Left Ventricle	heart
20	chr4:26914800-26921800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:26914800-26923400	Weak transcription	NHDF-Ad	bronchial
22	chr4:26914800-26924800	Weak transcription	Lung	lung
23	chr4:26914800-26925200	Weak transcription	NHLF	lung
24	chr4:26914800-26925800	Weak transcription	Colonic Mucosa	Colon
25	chr4:26914800-26926000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:26914800-26929200	Weak transcription	K562	blood
27	chr4:26914800-26929600	Weak transcription	Pancreas	Pancrea
28	chr4:26914800-26930000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr4:26914800-26932400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr4:26914800-26932600	Weak transcription	Spleen	Spleen
31	chr4:26914800-26942200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:26915200-26921600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr4:26915800-26924200	Weak transcription	Fetal Intestine Small	intestine
34	chr4:26917600-26925800	Weak transcription	Esophagus	oesophagus
35	chr4:26918000-26921600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr4:26918000-26926200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:26918200-26921600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:26918200-26921600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr4:26918200-26921600	Weak transcription	Brain Angular Gyrus	brain
40	chr4:26918200-26921600	Weak transcription	Ovary	ovary
41	chr4:26918200-26921600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:26918200-26921600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr4:26918200-26921600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr4:26918200-26923000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr4:26918200-26925400	Weak transcription	Gastric	stomach
46	chr4:26918200-26938400	Weak transcription	Psoas Muscle	Psoas
47	chr4:26918400-26921600	Weak transcription	Brain Anterior Caudate	brain
48	chr4:26918400-26939800	Weak transcription	Fetal Heart	heart
49	chr4:26919000-26921600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr4:26919200-26926400	Weak transcription	NH-A	brain

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