Variant report

Variant	rs4692137
Chromosome Location	chr4:27005235-27005236
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr4:27005155-27005750	GM12878	blood:	n/a	n/a
2	CTCF	chr4:27005200-27005350	HA-sp	spinal cord:	n/a	n/a
3	RUNX3	chr4:27005171-27005671	GM12878	blood:	n/a	n/a
4	NFIC	chr4:27005122-27005699	GM12878	blood:	n/a	n/a
5	CTCF	chr4:27005200-27005350	HVMF	connective:	n/a	n/a

Variant related genes	Relation type
STIM2	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10023256	0.81[CEU][hapmap]
rs10470822	0.89[CEU][hapmap]
rs10939144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12644232	0.85[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs13434709	0.81[CEU][hapmap]
rs17555311	0.92[CEU][hapmap]
rs4519791	0.89[CEU][hapmap]
rs4692132	0.81[CEU][hapmap]
rs6448485	0.96[CEU][hapmap]
rs6448487	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs6822297	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6831605	0.96[CEU][hapmap]
rs6847438	0.96[CEU][hapmap]
rs724624	0.90[ASW][hapmap];0.88[CEU][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs725981	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs7658174	0.96[CEU][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs7672936	0.89[CEU][hapmap]
rs7692953	0.92[CEU][hapmap]
rs9654110	0.81[CEU][hapmap]
rs9998368	0.96[CEU][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4692137	STIM2	cis	uninvolved skin	skin_eQTL
rs4692137	STIM2	cis	cerebellum	SCAN
rs4692137	STIM2	cis	Whole Blood	GTEx
rs4692137	STIM2	cis	normal skin	skin_eQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26978400-27019200	Weak transcription	Fetal Intestine Small	intestine
2	chr4:26980400-27019400	Weak transcription	Left Ventricle	heart
3	chr4:26985400-27019400	Weak transcription	Esophagus	oesophagus
4	chr4:26989000-27010000	Weak transcription	Thymus	Thymus
5	chr4:26989000-27010400	Weak transcription	Fetal Thymus	thymus
6	chr4:26989400-27024800	Weak transcription	Psoas Muscle	Psoas
7	chr4:26989600-27027000	Weak transcription	HepG2	liver
8	chr4:26994800-27011000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr4:26995000-27019000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:26995000-27028200	Weak transcription	Pancreas	Pancrea
11	chr4:26995200-27006600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:26995400-27009800	Weak transcription	Adipose Nuclei	Adipose
13	chr4:26996200-27015400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:26996400-27005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr4:26996400-27007600	Weak transcription	Brain Angular Gyrus	brain
16	chr4:26996400-27026200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:26996600-27007600	Weak transcription	Ovary	ovary
18	chr4:26996600-27011800	Weak transcription	Brain Anterior Caudate	brain
19	chr4:26996600-27018400	Weak transcription	Fetal Intestine Large	intestine
20	chr4:26996600-27019200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:26996800-27007200	Weak transcription	Brain Substantia Nigra	brain
22	chr4:26996800-27019200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:26997000-27007600	Weak transcription	Brain Hippocampus Middle	brain
24	chr4:26997200-27006400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:26997400-27019200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr4:27000400-27005400	Weak transcription	Osteobl	bone
27	chr4:27001200-27029600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:27001600-27006800	Weak transcription	Liver	Liver
29	chr4:27001600-27019000	Weak transcription	Spleen	Spleen
30	chr4:27002000-27005400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:27002000-27019200	Weak transcription	Lung	lung
32	chr4:27002000-27019200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr4:27002200-27006400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:27002200-27013000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:27002600-27006000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:27002600-27006600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr4:27002600-27011200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr4:27002800-27006000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:27002800-27011800	Weak transcription	Stomach Mucosa	stomach
40	chr4:27002800-27026000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr4:27003000-27005400	Weak transcription	HSMMtube	muscle
42	chr4:27003200-27006000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr4:27003400-27005400	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr4:27003400-27007800	Weak transcription	Aorta	Aorta
45	chr4:27003400-27011600	Strong transcription	Primary B cells from cord blood	blood
46	chr4:27003800-27005800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr4:27004000-27005400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:27004000-27011000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:27004200-27005400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr4:27004200-27006200	Strong transcription	Primary monocytes fromperipheralblood	blood

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