Variant report

Variant	rs28570016
Chromosome Location	chr4:26977754-26977755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:26977005..26979761-chr4:27016014..27017774,2	MCF-7	breast:
2	chr4:26862490..26864682-chr4:26976587..26979178,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109689	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10010180	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10433805	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12152700	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13140015	0.86[EUR][1000 genomes]
rs28668622	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2871258	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35499018	0.95[ASN][1000 genomes]
rs3762900	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4692136	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6448491	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6830950	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6838936	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7669818	0.95[ASN][1000 genomes]
rs7679403	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7680613	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7681802	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7693687	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7695335	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7700108	0.90[ASN][1000 genomes]
rs9291487	0.90[ASN][1000 genomes]
rs9995206	0.81[AMR][1000 genomes]
rs9998971	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];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	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
3	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
4	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
rs28570016	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26950000-26980200	Weak transcription	Spleen	Spleen
2	chr4:26950200-26979400	Weak transcription	Ovary	ovary
3	chr4:26961800-26980200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:26961800-26994000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr4:26963600-26994200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:26966600-26986400	Weak transcription	HSMM	muscle
7	chr4:26966600-26989000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:26966600-26994600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:26966800-26979200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:26966800-26979400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:26966800-26985200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr4:26966800-26986400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr4:26967000-26980000	Weak transcription	GM12878-XiMat	blood
14	chr4:26967600-26986400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:26969800-26979400	Weak transcription	Pancreas	Pancrea
16	chr4:26969800-26980000	Weak transcription	Primary B cells from cord blood	blood
17	chr4:26975800-26979200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr4:26975800-26980400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr4:26975800-27003200	Weak transcription	Aorta	Aorta
20	chr4:26976200-26978600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:26976600-26978800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr4:26977200-26977800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:26977200-26977800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:26977200-26977800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr4:26977200-26978000	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr4:26977200-26978000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr4:26977200-26978000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:26977200-26978000	Enhancers	Primary T cells fromperipheralblood	blood
29	chr4:26977200-26978000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr4:26977200-26978000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr4:26977200-26978000	Strong transcription	Fetal Stomach	stomach
32	chr4:26977200-26978000	Enhancers	Gastric	stomach
33	chr4:26977200-26978000	Enhancers	Lung	lung
34	chr4:26977200-26978000	Strong transcription	Thymus	Thymus
35	chr4:26977200-26978200	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr4:26977200-26978400	Strong transcription	Fetal Intestine Small	intestine
37	chr4:26977200-26980800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr4:26977400-26978800	Weak transcription	Brain Angular Gyrus	brain
39	chr4:26977400-26979000	Weak transcription	Primary T cells from cord blood	blood
40	chr4:26977600-26977800	ZNF genes & repeats	Fetal Thymus	thymus
41	chr4:26977600-26978000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr4:26977600-26978000	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr4:26977600-26978000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:26977600-26978600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr4:26977600-26978800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr4:26977600-26978800	Strong transcription	Fetal Muscle Leg	muscle
47	chr4:26977600-26979400	Weak transcription	Primary B cells from peripheral blood	blood

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