Variant report

Variant	rs11737218
Chromosome Location	chr4:26885773-26885774
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	chr4:26877548..26879443-chr4:26882952..26885822,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10023256	0.81[ASW][hapmap]
rs10029307	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]
rs11729927	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11730235	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11734308	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11943948	0.94[ASN][1000 genomes]
rs12641261	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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];0.95[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];0.96[ASN][1000 genomes]
rs12646473	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs12650172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13116341	0.87[ASN][1000 genomes]
rs13138942	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13139464	0.89[ASN][1000 genomes]
rs28497454	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28520489	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34996346	0.95[ASN][1000 genomes]
rs3792685	0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs3924178	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4274829	0.94[ASN][1000 genomes]
rs4407490	0.84[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4505809	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4519790	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4532223	0.94[ASN][1000 genomes]
rs4557250	0.94[ASN][1000 genomes]
rs4557251	0.93[ASN][1000 genomes]
rs57663175	0.93[ASN][1000 genomes]
rs57686546	0.91[ASN][1000 genomes]
rs58075729	0.87[ASN][1000 genomes]
rs58968032	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60890366	0.89[ASN][1000 genomes]
rs61047003	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62302532	0.87[ASN][1000 genomes]
rs62302533	0.87[ASN][1000 genomes]
rs62302535	0.86[ASN][1000 genomes]
rs6448479	0.94[ASN][1000 genomes]
rs6448484	0.95[ASN][1000 genomes]
rs6448488	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6815719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6833053	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6833895	0.94[ASN][1000 genomes]
rs6835631	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6844153	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6853032	0.94[ASN][1000 genomes]
rs73116683	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73811400	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73813220	0.93[ASN][1000 genomes]
rs7655686	0.94[ASN][1000 genomes]
rs9654110	0.81[ASW][hapmap]
rs9790789	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

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
rs11737218	STIM2	cis	lymphoblastoid	seeQTL
rs11737218	STIM2	cis	multi-tissue	Pritchard
rs11737218	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs11737218		cis	Lymphoblastoid	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26864400-26886600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr4:26869800-26886000	Weak transcription	Fetal Stomach	stomach
3	chr4:26873000-26886200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:26875600-26904600	Weak transcription	Brain Anterior Caudate	brain
5	chr4:26875800-26888200	Weak transcription	Adipose Nuclei	Adipose
6	chr4:26878600-26885800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr4:26880600-26902400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:26880600-26921600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr4:26881800-26886800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:26881800-26896200	Weak transcription	HMEC	breast
11	chr4:26882000-26885800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:26882000-26887800	Weak transcription	Stomach Mucosa	stomach
13	chr4:26882000-26897000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:26882200-26889000	Weak transcription	K562	blood
15	chr4:26882600-26885800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr4:26883000-26885800	Weak transcription	Brain Substantia Nigra	brain
17	chr4:26883400-26892800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr4:26883600-26887200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:26883800-26885800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:26884200-26885800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:26884200-26886400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr4:26884200-26886400	Weak transcription	Brain Hippocampus Middle	brain
23	chr4:26884600-26885800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr4:26884600-26886200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:26884600-26888000	Weak transcription	Spleen	Spleen
26	chr4:26885000-26887000	Enhancers	Fetal Heart	heart
27	chr4:26885000-26887600	Enhancers	Primary hematopoietic stem cells	blood
28	chr4:26885000-26887600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:26885200-26885800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:26885200-26886600	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr4:26885200-26888600	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr4:26885400-26885800	Enhancers	Brain Cingulate Gyrus	brain
33	chr4:26885400-26886000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr4:26885400-26886000	Enhancers	Fetal Kidney	kidney
35	chr4:26885400-26886000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr4:26885400-26886200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr4:26885400-26886600	Enhancers	Small Intestine	intestine
38	chr4:26885400-26887000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:26885400-26887000	Enhancers	Duodenum Mucosa	Duodenum
40	chr4:26885400-26887200	Flanking Active TSS	GM12878-XiMat	blood
41	chr4:26885400-26887400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr4:26885400-26887400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr4:26885400-26889200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr4:26885400-26889200	Flanking Active TSS	Dnd41	blood
45	chr4:26885600-26885800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:26885600-26885800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:26885600-26885800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr4:26885600-26885800	Enhancers	Fetal Lung	lung
49	chr4:26885600-26886000	Enhancers	Fetal Thymus	thymus
50	chr4:26885600-26886400	Enhancers	H9 Cell Line	embryonic stem cell

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