Variant report

Variant	rs12646473
Chromosome Location	chr4:26875455-26875456
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10029307	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11729927	0.92[ASN][1000 genomes]
rs11730235	1.00[CHB][hapmap];0.96[JPT][hapmap];0.92[ASN][1000 genomes]
rs11734308	0.89[ASN][1000 genomes]
rs11737218	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11943948	0.93[ASN][1000 genomes]
rs12641261	0.98[ASN][1000 genomes]
rs12644073	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12650172	0.95[CHB][hapmap];0.96[JPT][hapmap];0.98[ASN][1000 genomes]
rs13116341	0.87[ASN][1000 genomes]
rs13138942	0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs13139464	0.89[ASN][1000 genomes]
rs16878655	0.93[CEU][hapmap]
rs28497454	0.91[ASN][1000 genomes]
rs28520489	0.89[ASN][1000 genomes]
rs34996346	0.95[ASN][1000 genomes]
rs3792685	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3924178	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4274829	0.93[ASN][1000 genomes]
rs4407490	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4505809	0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4519790	0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs4532223	0.93[ASN][1000 genomes]
rs4557250	0.93[ASN][1000 genomes]
rs4557251	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57663175	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57686546	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58075729	0.86[ASN][1000 genomes]
rs58968032	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60890366	0.90[ASN][1000 genomes]
rs61047003	0.87[ASN][1000 genomes]
rs62302532	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62302533	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62302535	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6448479	0.94[ASN][1000 genomes]
rs6448484	0.96[ASN][1000 genomes]
rs6448488	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6815719	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs6833053	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs6833895	0.94[ASN][1000 genomes]
rs6835631	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6844153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6853032	0.94[ASN][1000 genomes]
rs73116683	0.86[ASN][1000 genomes]
rs73811400	0.97[ASN][1000 genomes]
rs73813220	0.93[ASN][1000 genomes]
rs7655686	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9790789	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12646473	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs12646473	STIM2	cis	multi-tissue	Pritchard
rs12646473		cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26864200-26876800	Weak transcription	Colonic Mucosa	Colon
2	chr4:26864200-26877200	Weak transcription	Aorta	Aorta
3	chr4:26864400-26886600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr4:26864600-26885600	Weak transcription	Thymus	Thymus
5	chr4:26865600-26876000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr4:26866000-26880400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr4:26866000-26881800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:26867200-26879000	Weak transcription	Fetal Intestine Small	intestine
9	chr4:26867200-26880000	Weak transcription	Fetal Intestine Large	intestine
10	chr4:26867200-26884200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:26869400-26876200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:26869600-26876000	Enhancers	Primary T cells from cord blood	blood
13	chr4:26869800-26877000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr4:26869800-26886000	Weak transcription	Fetal Stomach	stomach
15	chr4:26870000-26876400	Weak transcription	Brain Substantia Nigra	brain
16	chr4:26870000-26879400	Weak transcription	NHLF	lung
17	chr4:26870000-26879600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:26870400-26875800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:26870600-26881800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr4:26870800-26879200	Weak transcription	Small Intestine	intestine
21	chr4:26870800-26880800	Weak transcription	Stomach Mucosa	stomach
22	chr4:26871400-26876800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr4:26871600-26876800	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr4:26872200-26876000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:26872800-26877400	Weak transcription	HSMMtube	muscle
26	chr4:26873000-26886200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr4:26873200-26875800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:26873400-26875600	Enhancers	Primary B cells from cord blood	blood
29	chr4:26873400-26877800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:26873400-26883600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:26873600-26875800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:26873600-26875800	Weak transcription	Fetal Lung	lung
33	chr4:26873600-26876400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr4:26873600-26879200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:26873600-26880000	Weak transcription	NHEK	skin
36	chr4:26873800-26876200	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr4:26873800-26880000	Weak transcription	HMEC	breast
38	chr4:26873800-26881200	Weak transcription	Fetal Heart	heart
39	chr4:26873800-26881400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:26874000-26875600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:26874000-26875800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:26874200-26876000	Enhancers	Primary B cells from peripheral blood	blood
43	chr4:26874400-26875800	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr4:26874400-26875800	Enhancers	GM12878-XiMat	blood
45	chr4:26874400-26876000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:26874600-26875600	Enhancers	Primary hematopoietic stem cells	blood
47	chr4:26874600-26875600	Enhancers	Left Ventricle	heart
48	chr4:26874600-26876000	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr4:26874600-26876000	Enhancers	Spleen	Spleen
50	chr4:26874800-26875600	Enhancers	Placenta	Placenta

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