Variant report

Variant	rs10029307
Chromosome Location	chr4:26904213-26904214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:26903933..26906548-chr4:26914437..26916470,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10023256	0.81[ASW][hapmap]
rs11729927	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730235	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11734308	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11737218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11943948	0.88[ASN][1000 genomes]
rs12641261	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12644073	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12646473	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12650172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13116341	0.82[ASN][1000 genomes]
rs13138942	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13139464	0.84[ASN][1000 genomes]
rs28497454	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28520489	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34996346	0.89[ASN][1000 genomes]
rs3792685	0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs3924178	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4274829	0.88[ASN][1000 genomes]
rs4407490	0.81[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4505809	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4519790	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4532223	0.88[ASN][1000 genomes]
rs4557250	0.88[ASN][1000 genomes]
rs4557251	0.87[ASN][1000 genomes]
rs57663175	0.99[ASN][1000 genomes]
rs57686546	0.97[ASN][1000 genomes]
rs58075729	0.81[ASN][1000 genomes]
rs58968032	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60890366	0.94[ASN][1000 genomes]
rs61047003	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62302532	0.93[ASN][1000 genomes]
rs62302533	0.93[ASN][1000 genomes]
rs62302535	0.91[ASN][1000 genomes]
rs6448479	0.89[ASN][1000 genomes]
rs6448484	0.89[ASN][1000 genomes]
rs6448488	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6815719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6833053	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6833895	0.89[ASN][1000 genomes]
rs6835631	0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6844153	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6853032	0.89[ASN][1000 genomes]
rs73116683	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73811400	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73813220	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7655686	0.96[ASN][1000 genomes]
rs9654110	0.81[ASW][hapmap]
rs9790789	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10029307	STIM2	cis	lymphoblastoid	seeQTL
rs10029307	STIM2	cis	multi-tissue	Pritchard
rs10029307	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs10029307		cis	Lymphoblastoid	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26875600-26904600	Weak transcription	Brain Anterior Caudate	brain
2	chr4:26880600-26921600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:26886600-26921600	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:26889800-26906000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:26898400-26907400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:26898400-26914400	Weak transcription	HSMM	muscle
7	chr4:26899400-26905000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr4:26899400-26908000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr4:26899600-26904600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:26900400-26913200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:26900800-26908000	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr4:26901200-26907600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr4:26901600-26906800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr4:26901800-26909000	Weak transcription	GM12878-XiMat	blood
15	chr4:26902000-26906000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:26902000-26906000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:26902000-26906800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr4:26902600-26906000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:26902600-26906000	Weak transcription	Stomach Mucosa	stomach
20	chr4:26902600-26909000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:26902800-26905800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:26902800-26906000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr4:26902800-26906000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr4:26902800-26906000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr4:26902800-26906000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr4:26902800-26906000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr4:26902800-26906000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:26902800-26906000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr4:26902800-26906000	Weak transcription	Fetal Lung	lung
30	chr4:26902800-26906200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr4:26902800-26906200	Weak transcription	Adipose Nuclei	Adipose
32	chr4:26902800-26906400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:26902800-26906600	Weak transcription	Ovary	ovary
34	chr4:26902800-26907000	Weak transcription	Lung	lung
35	chr4:26902800-26908800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:26902800-26909400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr4:26902800-26909400	Weak transcription	Brain Substantia Nigra	brain
38	chr4:26902800-26909800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr4:26902800-26912400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr4:26902800-26914400	Weak transcription	Right Atrium	heart
41	chr4:26903000-26913000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:26903400-26905000	Strong transcription	Primary B cells from cord blood	blood
43	chr4:26903400-26905000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:26903600-26904400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:26903600-26904400	Enhancers	Left Ventricle	heart
46	chr4:26903600-26904400	Enhancers	Small Intestine	intestine
47	chr4:26903600-26904600	Genic enhancers	Primary T cells from cord blood	blood
48	chr4:26903600-26904800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr4:26903600-26905200	Enhancers	Brain Hippocampus Middle	brain
50	chr4:26903600-26909000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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