Variant report

Variant	rs9654110
Chromosome Location	chr4:26913094-26913095
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10006403	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10023256	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10029307	0.81[ASW][hapmap]
rs10939144	0.81[CEU][hapmap]
rs11737218	0.81[ASW][hapmap]
rs12331333	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12642608	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.98[ASN][1000 genomes]
rs12644073	0.80[ASW][hapmap]
rs12644232	0.80[JPT][hapmap]
rs13434709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17555311	0.81[CEU][hapmap]
rs4692132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4692137	0.81[CEU][hapmap]
rs6448478	0.81[JPT][hapmap]
rs6448485	0.85[CEU][hapmap]
rs6448487	0.85[CEU][hapmap]
rs6815719	0.81[ASW][hapmap]
rs6831605	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs6847438	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs7658174	0.85[CEU][hapmap]
rs7678705	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7692953	0.82[CEU][hapmap]
rs9654109	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9998368	0.85[CEU][hapmap];0.81[JPT][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
rs9654110	STIM2	cis	lymphoblastoid	seeQTL
rs9654110	STIM2	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

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	chr4:26898400-26914400	Weak transcription	HSMM	muscle
4	chr4:26900400-26913200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:26902800-26914400	Weak transcription	Right Atrium	heart
6	chr4:26904400-26913800	Weak transcription	Left Ventricle	heart
7	chr4:26907000-26913200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:26907000-26914400	Weak transcription	Psoas Muscle	Psoas
9	chr4:26907000-26917400	Weak transcription	Gastric	stomach
10	chr4:26907200-26913400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:26907200-26914000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:26907200-26914400	Weak transcription	Lung	lung
13	chr4:26907200-26937800	Weak transcription	Stomach Mucosa	stomach
14	chr4:26908400-26914800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr4:26909000-26915800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr4:26909600-26913200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:26909600-26916600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:26909600-26921400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:26909600-26923000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:26909800-26913200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr4:26909800-26921400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:26910000-26914200	Weak transcription	Fetal Lung	lung
23	chr4:26910000-26915800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:26910000-26916200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:26910000-26926600	Weak transcription	Fetal Stomach	stomach
26	chr4:26910200-26914000	Weak transcription	HSMMtube	muscle
27	chr4:26910200-26914200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:26910200-26914400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:26910200-26914400	Weak transcription	Adipose Nuclei	Adipose
30	chr4:26910200-26921000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr4:26910200-26921000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr4:26910200-26921200	Weak transcription	Primary B cells from cord blood	blood
33	chr4:26910200-26925800	Weak transcription	NHEK	skin
34	chr4:26910400-26914600	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr4:26910400-26921400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:26910600-26913200	Weak transcription	GM12878-XiMat	blood
37	chr4:26910800-26913800	Weak transcription	Small Intestine	intestine
38	chr4:26910800-26914400	Weak transcription	Pancreas	Pancrea
39	chr4:26910800-26921800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr4:26911000-26915000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr4:26911000-26915400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr4:26911000-26917400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:26911600-26914400	Weak transcription	Brain Angular Gyrus	brain
44	chr4:26911600-26965800	Weak transcription	HMEC	breast
45	chr4:26911800-26913400	Weak transcription	Brain Hippocampus Middle	brain
46	chr4:26911800-26914400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr4:26911800-26915000	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr4:26912000-26913200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr4:26912000-26913800	Weak transcription	Ovary	ovary
50	chr4:26912000-26914000	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links