Variant report

Variant	rs28445387
Chromosome Location	chr4:26863441-26863442
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr4:26862959-26863742	GM12878	blood:	n/a	n/a
2	YY1	chr4:26862994-26863517	GM12891	blood:	n/a	n/a
3	ZBTB7A	chr4:26862974-26863595	ECC-1	luminal epithelium:	n/a	n/a
4	SIN3A	chr4:26862065-26863574	GM12878	blood:	n/a	n/a
5	YY1	chr4:26861998-26863568	GM12892	blood:	n/a	n/a
6	MAX	chr4:26863153-26863608	Hela-S3	cervix:	n/a	n/a
7	ZNF143	chr4:26861819-26863610	GM12878	blood:	n/a	n/a
8	EP300	chr4:26861855-26863567	SK-N-SH	brain:	n/a	n/a
9	RCOR1	chr4:26862906-26863670	GM12878	blood:	n/a	n/a
10	MXI1	chr4:26861480-26863616	HepG2	liver:	n/a	n/a
11	MAX	chr4:26861760-26863605	GM12878	blood:	n/a	n/a
12	CHD2	chr4:26863079-26863618	GM12878	blood:	n/a	n/a
13	POLR2A	chr4:26861881-26863450	GM12892	blood:	n/a	n/a
14	MYC	chr4:26862862-26863535	NB4	blood:	n/a	n/a
15	POLR2A	chr4:26862902-26863459	GM12891	blood:	n/a	n/a
16	POU2F2	chr4:26862999-26863535	GM12891	blood:	n/a	n/a
17	RCOR1	chr4:26863125-26863533	K562	blood:	n/a	n/a
18	TCF7L2	chr4:26863238-26863766	HEK293	kidney:	n/a	n/a
19	TCF7L2	chr4:26863109-26863643	Hela-S3	cervix:	n/a	n/a
20	SIN3AK20	chr4:26863021-26863647	MCF-7	breast:	n/a	n/a
21	CTBP2	chr4:26861766-26863483	H1-hESC	embryonic stem cell:	n/a	n/a
22	EBF1	chr4:26862674-26863671	GM12878	blood:	n/a	chr4:26863457-26863468 chr4:26863458-26863468 chr4:26863458-26863467
23	CTCF	chr4:26863360-26863510	HRE	kidney:	n/a	chr4:26863501-26863508
24	ZNF384	chr4:26863118-26863718	GM12878	blood:	n/a	chr4:26863350-26863358
25	CHD1	chr4:26861257-26864940	IMR90	lung:	n/a	n/a
26	UBTF	chr4:26861897-26863750	K562	blood:	n/a	n/a
27	PAX5	chr4:26862750-26863551	GM12878	blood:	n/a	chr4:26863132-26863151
28	SIN3A	chr4:26861486-26863615	H1-hESC	embryonic stem cell:	n/a	n/a
29	YY1	chr4:26862317-26863520	GM12878	blood:	n/a	n/a
30	ELF1	chr4:26861878-26863464	GM12878	blood:	n/a	chr4:26862237-26862246
31	FOXM1	chr4:26862934-26863541	GM12878	blood:	n/a	n/a
32	RCOR1	chr4:26861624-26863701	K562	blood:	n/a	n/a
33	POU2F2	chr4:26863029-26863669	GM12878	blood:	n/a	n/a
34	ELF1	chr4:26861937-26863513	GM12878	blood:	n/a	chr4:26862237-26862246
35	EBF1	chr4:26863050-26863770	GM12878	blood:	n/a	chr4:26863457-26863468 chr4:26863458-26863468 chr4:26863458-26863467
36	POLR2A	chr4:26861807-26863480	NB4	blood:	n/a	n/a
37	ZNF384	chr4:26862000-26863736	K562	blood:	n/a	chr4:26863350-26863358
38	MAZ	chr4:26861763-26863639	IMR90	lung:	n/a	n/a
39	WRNIP1	chr4:26863195-26863713	GM12878	blood:	n/a	n/a
40	TBL1XR1	chr4:26863050-26863597	GM12878	blood:	n/a	n/a
41	POLR2A	chr4:26861837-26863647	H1-neurons	neurons:	n/a	n/a
42	POLR2A	chr4:26863013-26863622	GM12878	blood:	n/a	n/a
43	CTCF	chr4:26861660-26863595	SK-N-SH	brain:	n/a	chr4:26863501-26863508
44	CTCF	chr4:26863420-26863570	SK-N-SH_RA	brain:	n/a	chr4:26863501-26863508
45	RAD21	chr4:26862659-26863602	H1-hESC	embryonic stem cell:	n/a	chr4:26863409-26863421
46	TCF12	chr4:26863015-26863523	GM12878	blood:	n/a	chr4:26863410-26863417
47	MAZ	chr4:26863022-26863461	GM12878	blood:	n/a	n/a
48	POLR2A	chr4:26861831-26863562	GM18505	blood:	n/a	n/a
49	EP300	chr4:26863067-26863500	GM12878	blood:	n/a	n/a
50	RUNX3	chr4:26862740-26863788	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42054703..42055601-chr4:26863001..26863501,2	NB4	blood:

Variant related genes	Relation type
ENSG00000240005	TF binding region
ENSG00000182606	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12648414	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12648597	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3924177	0.82[EUR][1000 genomes]
rs4133239	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4259045	0.82[EUR][1000 genomes]
rs4376128	0.83[EUR][1000 genomes]
rs4518229	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4519791	0.97[ASN][1000 genomes]
rs4575981	0.83[EUR][1000 genomes]
rs4692128	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4692129	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6448478	0.83[EUR][1000 genomes]
rs6448482	0.83[EUR][1000 genomes]
rs6448483	0.83[EUR][1000 genomes]
rs6448486	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6830323	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6830424	0.81[EUR][1000 genomes]
rs7672936	0.95[ASN][1000 genomes]
rs7678576	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7688788	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7697626	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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	esv3403917	chr4:26861379-26864227	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28445387	STIM2	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26860200-26864600	Active TSS	Fetal Muscle Trunk	muscle
2	chr4:26861200-26864000	Active TSS	Fetal Kidney	kidney
3	chr4:26861400-26864200	Active TSS	H1 Cell Line	embryonic stem cell
4	chr4:26861400-26864400	Active TSS	Rectal Smooth Muscle	rectum
5	chr4:26861600-26863800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:26861600-26863800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:26861600-26863800	Active TSS	Gastric	stomach
8	chr4:26861600-26863800	Active TSS	Pancreas	Pancrea
9	chr4:26861600-26863800	Active TSS	Right Ventricle	heart
10	chr4:26861600-26864000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr4:26861600-26864000	Active TSS	Psoas Muscle	Psoas
12	chr4:26861600-26864200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:26861600-26864200	Active TSS	Aorta	Aorta
14	chr4:26861600-26864200	Active TSS	Fetal Intestine Large	intestine
15	chr4:26861600-26864200	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr4:26861600-26864400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:26861600-26864600	Active TSS	HSMM	muscle
18	chr4:26861600-26864800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:26861600-26865400	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr4:26861600-26865400	Active TSS	Right Atrium	heart
21	chr4:26861600-26865800	Active TSS	NHLF	lung
22	chr4:26861800-26863600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:26861800-26863600	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr4:26861800-26863600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:26861800-26863600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:26861800-26863600	Active TSS	Placenta Amnion	Placenta Amnion
27	chr4:26861800-26863600	Active TSS	Osteobl	bone
28	chr4:26861800-26863800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:26861800-26863800	Active TSS	H9 Cell Line	embryonic stem cell
30	chr4:26861800-26863800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:26861800-26863800	Active TSS	Esophagus	oesophagus
32	chr4:26861800-26863800	Active TSS	Left Ventricle	heart
33	chr4:26861800-26863800	Active TSS	Lung	lung
34	chr4:26861800-26863800	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr4:26861800-26863800	Active TSS	Small Intestine	intestine
36	chr4:26861800-26863800	Active TSS	Stomach Mucosa	stomach
37	chr4:26861800-26864000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:26861800-26864000	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr4:26861800-26864000	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr4:26861800-26864000	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr4:26861800-26864000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr4:26861800-26864000	Active TSS	Brain Anterior Caudate	brain
43	chr4:26861800-26864000	Active TSS	Fetal Lung	lung
44	chr4:26861800-26864000	Active TSS	A549	lung
45	chr4:26861800-26864200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:26861800-26864200	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr4:26861800-26864200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr4:26861800-26864200	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr4:26861800-26864200	Active TSS	Brain Angular Gyrus	brain
50	chr4:26861800-26864200	Active TSS	Brain Cingulate Gyrus	brain

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