Variant report

Variant	rs11727649
Chromosome Location	chr4:26914837-26914838
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	chr4:26914621..26917099-chr4:26917825..26919349,2	K562	blood:
2	chr4:26903933..26906548-chr4:26914437..26916470,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10030655	0.81[CEU][hapmap]
rs10470823	0.81[CEU][hapmap]
rs10939141	0.81[CEU][hapmap]
rs11727039	1.00[ASW][hapmap];0.83[CHB][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap]
rs12505133	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13127603	0.81[CEU][hapmap]
rs4302449	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4586918	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55809332	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7667007	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7691908	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9999056	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11727649	STIM2	cis	cerebellum	SCAN
rs11727649	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 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	chr4:26907000-26917400	Weak transcription	Gastric	stomach
4	chr4:26907200-26937800	Weak transcription	Stomach Mucosa	stomach
5	chr4:26909000-26915800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr4:26909600-26916600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:26909600-26921400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:26909600-26923000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:26909800-26921400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:26910000-26915800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:26910000-26916200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:26910000-26926600	Weak transcription	Fetal Stomach	stomach
13	chr4:26910200-26921000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr4:26910200-26921000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr4:26910200-26921200	Weak transcription	Primary B cells from cord blood	blood
16	chr4:26910200-26925800	Weak transcription	NHEK	skin
17	chr4:26910400-26921400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:26910800-26921800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:26911000-26915000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr4:26911000-26915400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:26911000-26917400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:26911600-26965800	Weak transcription	HMEC	breast
23	chr4:26911800-26915000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr4:26912000-26915800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr4:26912400-26918800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:26912600-26921600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:26912800-26919600	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr4:26913000-26915000	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr4:26913000-26920200	Enhancers	Primary T cells from cord blood	blood
30	chr4:26913200-26915000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr4:26913800-26915000	Enhancers	Primary T cells fromperipheralblood	blood
32	chr4:26914000-26915200	Enhancers	Duodenum Mucosa	Duodenum
33	chr4:26914000-26923000	Weak transcription	Aorta	Aorta
34	chr4:26914200-26924200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:26914400-26917400	Weak transcription	Brain Substantia Nigra	brain
36	chr4:26914600-26915000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr4:26914600-26917400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:26914600-26917400	Weak transcription	Colon Smooth Muscle	Colon
39	chr4:26914600-26917400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr4:26914600-26921000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:26914600-26921600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:26914600-26921600	Weak transcription	Fetal Intestine Large	intestine
43	chr4:26914600-26921600	Weak transcription	Thymus	Thymus
44	chr4:26914600-26921800	Weak transcription	Fetal Brain Male	brain
45	chr4:26914600-26924800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr4:26914600-26936800	Weak transcription	Small Intestine	intestine
47	chr4:26914800-26915600	Enhancers	Fetal Lung	lung
48	chr4:26914800-26916200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr4:26914800-26916400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:26914800-26916400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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