Variant report

Variant	rs7655631
Chromosome Location	chr4:26869338-26869339
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:26867383..26869599-chr4:26869869..26871933,2	K562	blood:
2	chr4:26861373..26864331-chr4:26865426..26869825,6	K562	blood:
3	chr4:26864497..26869713-chr4:26871452..26874672,4	K562	blood:

Variant related genes	Relation type
ENSG00000240005	Chromatin interaction
ENSG00000109689	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10004120	0.90[EUR][1000 genomes]
rs10007132	0.85[CEU][hapmap]
rs10022599	0.90[CEU][hapmap]
rs10030655	0.95[CEU][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes]
rs10433805	0.90[CEU][hapmap]
rs10470823	0.95[CEU][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes]
rs10939140	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10939141	0.95[CEU][hapmap]
rs1122045	0.90[CEU][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11722323	0.82[CEU][hapmap]
rs12331378	0.85[CEU][hapmap]
rs13114545	0.81[CEU][hapmap]
rs13115054	0.80[CEU][hapmap]
rs13127603	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs13152367	0.80[EUR][1000 genomes]
rs28391037	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34506340	0.85[AFR][1000 genomes]
rs4692136	0.85[CEU][hapmap]
rs6830950	0.90[CEU][hapmap]
rs7664810	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7688454	0.91[ASN][1000 genomes]
rs7688662	0.81[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7693687	0.90[CEU][hapmap]
rs7695335	0.90[CEU][hapmap]
rs9998009	0.80[CEU][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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7655631	STIM2	cis	multi-tissue	Pritchard
rs7655631	STIM2	cis	uninvolved skin	skin_eQTL
rs7655631	RP11-293A21.1	cis	Skin Sun Exposed Lower leg	GTEx
rs7655631	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26863800-26869400	Weak transcription	Pancreas	Pancrea
2	chr4:26863800-26869400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:26863800-26870600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:26863800-26874600	Weak transcription	Left Ventricle	heart
5	chr4:26863800-26874600	Weak transcription	Spleen	Spleen
6	chr4:26863800-26875400	Weak transcription	Lung	lung
7	chr4:26864200-26876800	Weak transcription	Colonic Mucosa	Colon
8	chr4:26864200-26877200	Weak transcription	Aorta	Aorta
9	chr4:26864400-26869400	Weak transcription	Fetal Thymus	thymus
10	chr4:26864400-26869800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:26864400-26872600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:26864400-26873400	Weak transcription	A549	lung
13	chr4:26864400-26886600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr4:26864600-26869400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr4:26864600-26869400	Weak transcription	Brain Germinal Matrix	brain
16	chr4:26864600-26869400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr4:26864600-26869600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:26864600-26870800	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr4:26864600-26870800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:26864600-26871000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr4:26864600-26871800	Enhancers	Primary B cells from peripheral blood	blood
22	chr4:26864600-26872600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr4:26864600-26885600	Weak transcription	Thymus	Thymus
24	chr4:26864800-26869400	Weak transcription	NH-A	brain
25	chr4:26864800-26871200	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr4:26864800-26872600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:26865000-26870600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr4:26865200-26869400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:26865200-26873000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:26865200-26873200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:26865400-26869400	Weak transcription	Fetal Muscle Leg	muscle
32	chr4:26865400-26869600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:26865600-26869400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr4:26865600-26869400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:26865600-26869400	Weak transcription	Fetal Stomach	stomach
36	chr4:26865600-26869800	Enhancers	Brain Angular Gyrus	brain
37	chr4:26865600-26870000	Enhancers	Dnd41	blood
38	chr4:26865600-26876000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr4:26865800-26869400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:26865800-26870600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr4:26865800-26872400	Weak transcription	HSMMtube	muscle
42	chr4:26865800-26872600	Weak transcription	HSMM	muscle
43	chr4:26866000-26872600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:26866000-26880400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr4:26866000-26881800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:26866400-26870200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:26866600-26870800	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr4:26866800-26869400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:26866800-26869400	Weak transcription	HUVEC	blood vessel
50	chr4:26866800-26869600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links