Variant report

Variant	rs11730235
Chromosome Location	chr4:26924444-26924445
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:26917818..26920281-chr4:26922322..26924657,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10029307	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11729927	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734308	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11737218	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11943948	0.87[ASN][1000 genomes]
rs12641261	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12644073	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12646473	1.00[CHB][hapmap];0.96[JPT][hapmap];0.92[ASN][1000 genomes]
rs12650172	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13116341	0.81[ASN][1000 genomes]
rs13138942	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13139464	0.83[ASN][1000 genomes]
rs28497454	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28520489	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34996346	0.89[ASN][1000 genomes]
rs3792685	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs3924178	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4274829	0.87[ASN][1000 genomes]
rs4407490	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4505809	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4519790	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4532223	0.87[ASN][1000 genomes]
rs4557250	0.87[ASN][1000 genomes]
rs4557251	0.86[ASN][1000 genomes]
rs57663175	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs57686546	0.99[ASN][1000 genomes]
rs58075729	0.80[ASN][1000 genomes]
rs58968032	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60890366	0.96[ASN][1000 genomes]
rs61047003	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62302532	0.95[ASN][1000 genomes]
rs62302533	0.95[ASN][1000 genomes]
rs62302535	0.93[ASN][1000 genomes]
rs6448479	0.88[ASN][1000 genomes]
rs6448484	0.90[ASN][1000 genomes]
rs6448488	1.00[CHB][hapmap];0.96[JPT][hapmap];0.95[ASN][1000 genomes]
rs6815719	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6833053	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6833895	0.88[ASN][1000 genomes]
rs6835631	0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6844153	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6853032	0.89[ASN][1000 genomes]
rs73116683	0.94[ASN][1000 genomes]
rs73811400	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73813220	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7655686	0.97[ASN][1000 genomes]
rs9790789	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11730235	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs11730235		cis	Lymphoblastoid	GTEx
rs11730235	STIM2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26907200-26937800	Weak transcription	Stomach Mucosa	stomach
2	chr4:26910000-26926600	Weak transcription	Fetal Stomach	stomach
3	chr4:26910200-26925800	Weak transcription	NHEK	skin
4	chr4:26911600-26965800	Weak transcription	HMEC	breast
5	chr4:26914600-26924800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:26914600-26936800	Weak transcription	Small Intestine	intestine
7	chr4:26914800-26924800	Weak transcription	Lung	lung
8	chr4:26914800-26925200	Weak transcription	NHLF	lung
9	chr4:26914800-26925800	Weak transcription	Colonic Mucosa	Colon
10	chr4:26914800-26926000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:26914800-26929200	Weak transcription	K562	blood
12	chr4:26914800-26929600	Weak transcription	Pancreas	Pancrea
13	chr4:26914800-26930000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:26914800-26932400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr4:26914800-26932600	Weak transcription	Spleen	Spleen
16	chr4:26914800-26942200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:26917600-26925800	Weak transcription	Esophagus	oesophagus
18	chr4:26918000-26926200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:26918200-26925400	Weak transcription	Gastric	stomach
20	chr4:26918200-26938400	Weak transcription	Psoas Muscle	Psoas
21	chr4:26918400-26939800	Weak transcription	Fetal Heart	heart
22	chr4:26919200-26926400	Weak transcription	NH-A	brain
23	chr4:26919600-26932800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:26919800-26927000	Weak transcription	HepG2	liver
25	chr4:26920000-26926800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:26920200-26924600	Strong transcription	Dnd41	blood
27	chr4:26921000-26924600	Strong transcription	Primary B cells from peripheral blood	blood
28	chr4:26921000-26924600	Strong transcription	Primary T cells from cord blood	blood
29	chr4:26921000-26924600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr4:26921000-26924600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:26921000-26924600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:26921200-26924600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr4:26921200-26924600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr4:26921200-26924600	Strong transcription	Fetal Thymus	thymus
35	chr4:26921400-26924600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:26921400-26924600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:26921800-26932400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:26922200-26925800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:26922200-26932400	Weak transcription	Fetal Kidney	kidney
40	chr4:26922400-26925600	Weak transcription	Fetal Brain Female	brain
41	chr4:26922400-26926200	Weak transcription	Brain Anterior Caudate	brain
42	chr4:26922400-26927400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr4:26922600-26932600	Weak transcription	Brain Substantia Nigra	brain
44	chr4:26922800-26926000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr4:26922800-26941400	Weak transcription	Brain Hippocampus Middle	brain
46	chr4:26923000-26932400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr4:26923000-26940200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr4:26923000-26942400	Weak transcription	Fetal Brain Male	brain
49	chr4:26923000-26942400	Weak transcription	Left Ventricle	heart
50	chr4:26923200-26924800	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links