Variant report

Variant	rs1012550
Chromosome Location	chr4:26996007-26996008
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10007132	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10010180	0.95[CEU][hapmap]
rs10019691	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10939147	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12152700	0.96[CEU][hapmap]
rs12331378	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13115054	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs13140015	0.94[ASN][1000 genomes]
rs16878653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16878671	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28572642	0.82[ASN][1000 genomes]
rs2871256	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35499018	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3762900	0.95[CEU][hapmap]
rs4692136	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4692142	0.81[EUR][1000 genomes]
rs6833149	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6855865	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6856381	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7695335	0.81[CEU][hapmap]
rs7700108	0.91[CEU][hapmap]
rs9291487	0.96[CEU][hapmap]
rs9998009	1.00[CHB][hapmap];0.94[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1012550	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs1012550	STIM2	cis	normal skin	skin_eQTL
rs1012550	STIM2	cis	uninvolved skin	skin_eQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26975800-27003200	Weak transcription	Aorta	Aorta
2	chr4:26978400-27019200	Weak transcription	Fetal Intestine Small	intestine
3	chr4:26980400-27019400	Weak transcription	Left Ventricle	heart
4	chr4:26985400-27019400	Weak transcription	Esophagus	oesophagus
5	chr4:26988400-26998000	Weak transcription	Dnd41	blood
6	chr4:26989000-27010000	Weak transcription	Thymus	Thymus
7	chr4:26989000-27010400	Weak transcription	Fetal Thymus	thymus
8	chr4:26989400-26997000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:26989400-27024800	Weak transcription	Psoas Muscle	Psoas
10	chr4:26989600-27027000	Weak transcription	HepG2	liver
11	chr4:26993200-26996800	Enhancers	Fetal Lung	lung
12	chr4:26993200-26997000	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr4:26993200-26997200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr4:26993400-26996200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr4:26993400-26996800	Enhancers	Colon Smooth Muscle	Colon
16	chr4:26993400-26997000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr4:26993400-26997000	Enhancers	Brain Hippocampus Middle	brain
18	chr4:26993400-26997200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:26993400-26997200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr4:26993400-26997200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:26993400-26997400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr4:26993400-26997800	Enhancers	Primary T cells from cord blood	blood
23	chr4:26993800-26996600	Enhancers	Brain Anterior Caudate	brain
24	chr4:26994000-26996400	Enhancers	Brain Angular Gyrus	brain
25	chr4:26994000-26996800	Enhancers	Brain Substantia Nigra	brain
26	chr4:26994000-26997200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr4:26994200-26996600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:26994200-26996600	Enhancers	HSMMtube	muscle
29	chr4:26994200-26996800	Enhancers	Brain Cingulate Gyrus	brain
30	chr4:26994200-26996800	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr4:26994200-27004600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr4:26994400-26996400	Enhancers	HSMM	muscle
33	chr4:26994400-26996400	Enhancers	NHLF	lung
34	chr4:26994400-26997000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr4:26994600-26996600	Enhancers	Ovary	ovary
36	chr4:26994600-26996800	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr4:26994800-26996200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr4:26994800-26996200	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr4:26994800-26996200	Flanking Active TSS	GM12878-XiMat	blood
40	chr4:26994800-26997000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:26994800-26999000	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr4:26994800-27002600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:26994800-27004600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr4:26994800-27005200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:26994800-27011000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr4:26995000-26996600	Enhancers	Fetal Heart	heart
47	chr4:26995000-27002600	Weak transcription	Fetal Kidney	kidney
48	chr4:26995000-27002600	Weak transcription	Fetal Muscle Leg	muscle
49	chr4:26995000-27004000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:26995000-27004200	Weak transcription	Primary monocytes fromperipheralblood	blood

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