Variant report

Variant	rs12650172
Chromosome Location	chr4:26874406-26874407
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:26864497..26869713-chr4:26871452..26874672,4	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10029307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11729927	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11730235	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11734308	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11737218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11943948	0.94[ASN][1000 genomes]
rs12641261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12646473	0.95[CHB][hapmap];0.96[JPT][hapmap];0.98[ASN][1000 genomes]
rs13116341	0.88[ASN][1000 genomes]
rs13138942	0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13139464	0.90[ASN][1000 genomes]
rs28497454	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28520489	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34996346	0.96[ASN][1000 genomes]
rs3792685	0.90[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs3924178	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4274829	0.94[ASN][1000 genomes]
rs4407490	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4505809	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4519790	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4532223	0.94[ASN][1000 genomes]
rs4557250	0.94[ASN][1000 genomes]
rs4557251	0.93[ASN][1000 genomes]
rs57663175	0.92[ASN][1000 genomes]
rs57686546	0.91[ASN][1000 genomes]
rs58075729	0.87[ASN][1000 genomes]
rs58968032	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60890366	0.88[ASN][1000 genomes]
rs61047003	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62302532	0.87[ASN][1000 genomes]
rs62302533	0.86[ASN][1000 genomes]
rs62302535	0.85[ASN][1000 genomes]
rs6448479	0.95[ASN][1000 genomes]
rs6448484	0.96[ASN][1000 genomes]
rs6448488	0.95[CHB][hapmap];0.96[JPT][hapmap];0.86[ASN][1000 genomes]
rs6815719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833053	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833895	0.95[ASN][1000 genomes]
rs6835631	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6844153	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6853032	0.94[ASN][1000 genomes]
rs73116683	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73811400	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73813220	0.92[ASN][1000 genomes]
rs7655686	0.93[ASN][1000 genomes]
rs9790789	0.86[CHB][hapmap];1.00[JPT][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
rs12650172	STIM2	cis	multi-tissue	Pritchard
rs12650172		cis	Lymphoblastoid	GTEx
rs12650172	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26863800-26874600	Weak transcription	Left Ventricle	heart
2	chr4:26863800-26874600	Weak transcription	Spleen	Spleen
3	chr4:26863800-26875400	Weak transcription	Lung	lung
4	chr4:26864200-26876800	Weak transcription	Colonic Mucosa	Colon
5	chr4:26864200-26877200	Weak transcription	Aorta	Aorta
6	chr4:26864400-26886600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr4:26864600-26885600	Weak transcription	Thymus	Thymus
8	chr4:26865600-26876000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr4:26866000-26880400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr4:26866000-26881800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:26867200-26879000	Weak transcription	Fetal Intestine Small	intestine
12	chr4:26867200-26880000	Weak transcription	Fetal Intestine Large	intestine
13	chr4:26867200-26884200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:26869400-26876200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:26869600-26874600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:26869600-26876000	Enhancers	Primary T cells from cord blood	blood
17	chr4:26869800-26874600	Weak transcription	Brain Angular Gyrus	brain
18	chr4:26869800-26875400	Weak transcription	Pancreas	Pancrea
19	chr4:26869800-26877000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr4:26869800-26886000	Weak transcription	Fetal Stomach	stomach
21	chr4:26870000-26874600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr4:26870000-26875000	Weak transcription	Brain Anterior Caudate	brain
23	chr4:26870000-26875000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:26870000-26875000	Weak transcription	Fetal Muscle Leg	muscle
25	chr4:26870000-26875000	Weak transcription	Fetal Thymus	thymus
26	chr4:26870000-26875200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:26870000-26875200	Weak transcription	Adipose Nuclei	Adipose
28	chr4:26870000-26876400	Weak transcription	Brain Substantia Nigra	brain
29	chr4:26870000-26879400	Weak transcription	NHLF	lung
30	chr4:26870000-26879600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr4:26870200-26874800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr4:26870400-26875800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr4:26870600-26881800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr4:26870800-26874800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:26870800-26875000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr4:26870800-26879200	Weak transcription	Small Intestine	intestine
37	chr4:26870800-26880800	Weak transcription	Stomach Mucosa	stomach
38	chr4:26871000-26875400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr4:26871000-26875400	Weak transcription	Psoas Muscle	Psoas
40	chr4:26871200-26875000	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr4:26871400-26876800	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr4:26871600-26876800	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr4:26872200-26876000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:26872800-26874800	Weak transcription	Placenta	Placenta
45	chr4:26872800-26877400	Weak transcription	HSMMtube	muscle
46	chr4:26873000-26886200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr4:26873200-26875800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:26873400-26875000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr4:26873400-26875600	Enhancers	Primary B cells from cord blood	blood
50	chr4:26873400-26877800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links