Variant report

Variant	rs11729927
Chromosome Location	chr4:26923800-26923801
allele	A/C
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: 1 )

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

rs_ID	r²[population]
rs10029307	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730235	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734308	0.95[ASN][1000 genomes]
rs11737218	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11943948	0.87[ASN][1000 genomes]
rs12641261	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12644073	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12646473	0.92[ASN][1000 genomes]
rs12650172	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13116341	0.81[ASN][1000 genomes]
rs13138942	0.90[ASN][1000 genomes]
rs13139464	0.83[ASN][1000 genomes]
rs28497454	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28520489	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34996346	0.89[ASN][1000 genomes]
rs3792685	0.92[ASN][1000 genomes]
rs3924178	0.81[ASN][1000 genomes]
rs4274829	0.87[ASN][1000 genomes]
rs4407490	0.80[ASN][1000 genomes]
rs4505809	0.90[ASN][1000 genomes]
rs4519790	0.87[ASN][1000 genomes]
rs4532223	0.87[ASN][1000 genomes]
rs4557250	0.87[ASN][1000 genomes]
rs4557251	0.86[ASN][1000 genomes]
rs57663175	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs57686546	0.99[ASN][1000 genomes]
rs58075729	0.80[ASN][1000 genomes]
rs58968032	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60890366	0.96[ASN][1000 genomes]
rs61047003	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62302532	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62302533	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62302535	0.93[ASN][1000 genomes]
rs6448479	0.88[ASN][1000 genomes]
rs6448484	0.90[ASN][1000 genomes]
rs6448488	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6815719	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6833053	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6833895	0.88[ASN][1000 genomes]
rs6835631	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6844153	0.96[ASN][1000 genomes]
rs6853032	0.89[ASN][1000 genomes]
rs73116683	0.94[ASN][1000 genomes]
rs73811400	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73813220	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7655686	0.97[ASN][1000 genomes]
rs9790789	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11729927	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

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	chr4:26914200-26924200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:26914600-26924800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:26914600-26936800	Weak transcription	Small Intestine	intestine
8	chr4:26914800-26924800	Weak transcription	Lung	lung
9	chr4:26914800-26925200	Weak transcription	NHLF	lung
10	chr4:26914800-26925800	Weak transcription	Colonic Mucosa	Colon
11	chr4:26914800-26926000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:26914800-26929200	Weak transcription	K562	blood
13	chr4:26914800-26929600	Weak transcription	Pancreas	Pancrea
14	chr4:26914800-26930000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:26914800-26932400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr4:26914800-26932600	Weak transcription	Spleen	Spleen
17	chr4:26914800-26942200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:26915800-26924200	Weak transcription	Fetal Intestine Small	intestine
19	chr4:26917600-26925800	Weak transcription	Esophagus	oesophagus
20	chr4:26918000-26926200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:26918200-26925400	Weak transcription	Gastric	stomach
22	chr4:26918200-26938400	Weak transcription	Psoas Muscle	Psoas
23	chr4:26918400-26939800	Weak transcription	Fetal Heart	heart
24	chr4:26919200-26926400	Weak transcription	NH-A	brain
25	chr4:26919600-26932800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:26919800-26927000	Weak transcription	HepG2	liver
27	chr4:26920000-26926800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:26920200-26924000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr4:26920200-26924600	Strong transcription	Dnd41	blood
30	chr4:26921000-26923800	Strong transcription	Fetal Lung	lung
31	chr4:26921000-26924000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr4:26921000-26924000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr4:26921000-26924200	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr4:26921000-26924400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr4:26921000-26924400	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr4:26921000-26924400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
37	chr4:26921000-26924600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr4:26921000-26924600	Strong transcription	Primary T cells from cord blood	blood
39	chr4:26921000-26924600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr4:26921000-26924600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:26921000-26924600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:26921200-26923800	Strong transcription	Primary hematopoietic stem cells	blood
43	chr4:26921200-26924000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:26921200-26924000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:26921200-26924400	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr4:26921200-26924400	Strong transcription	Primary B cells from cord blood	blood
47	chr4:26921200-26924400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr4:26921200-26924600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr4:26921200-26924600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr4:26921200-26924600	Strong transcription	Fetal Thymus	thymus

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