Variant report

Variant	rs28391037
Chromosome Location	chr4:26866972-26866973
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	POLR2A	chr4:26866609-26867026	GM12891	blood:	n/a	n/a
2	POLR2A	chr4:26866575-26867125	K562	blood:	n/a	n/a
3	GATA3	chr4:26866757-26867049	SH-SY5Y	brain:	n/a	n/a
4	POLR2A	chr4:26866623-26867096	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:26861373..26864331-chr4:26865426..26869825,6	K562	blood:
2	chr4:26864497..26869713-chr4:26871452..26874672,4	K562	blood:

Variant related genes	Relation type
ENSG00000240005	TF binding region
ENSG00000109689	Chromatin interaction
ENSG00000240005	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10004120	0.82[EUR][1000 genomes]
rs10022599	0.81[EUR][1000 genomes]
rs10939140	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10939141	0.81[EUR][1000 genomes]
rs13147585	0.80[EUR][1000 genomes]
rs7655631	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7664810	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7688454	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7688662	0.84[EUR][1000 genomes];0.93[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28391037	RP11-293A21.1	cis	Skin Sun Exposed Lower leg	GTEx
rs28391037	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26861800-26867000	Active TSS	Ovary	ovary
2	chr4:26863800-26869400	Weak transcription	Pancreas	Pancrea
3	chr4:26863800-26869400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:26863800-26870600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:26863800-26874600	Weak transcription	Left Ventricle	heart
6	chr4:26863800-26874600	Weak transcription	Spleen	Spleen
7	chr4:26863800-26875400	Weak transcription	Lung	lung
8	chr4:26864000-26867800	Weak transcription	Psoas Muscle	Psoas
9	chr4:26864200-26876800	Weak transcription	Colonic Mucosa	Colon
10	chr4:26864200-26877200	Weak transcription	Aorta	Aorta
11	chr4:26864400-26869400	Weak transcription	Fetal Thymus	thymus
12	chr4:26864400-26869800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:26864400-26872600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:26864400-26873400	Weak transcription	A549	lung
15	chr4:26864400-26886600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:26864600-26867200	Enhancers	Brain Substantia Nigra	brain
17	chr4:26864600-26867200	Enhancers	Fetal Lung	lung
18	chr4:26864600-26867800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr4:26864600-26869200	Weak transcription	Fetal Kidney	kidney
20	chr4:26864600-26869400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr4:26864600-26869400	Weak transcription	Brain Germinal Matrix	brain
22	chr4:26864600-26869400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr4:26864600-26869600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:26864600-26870800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr4:26864600-26870800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr4:26864600-26871000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr4:26864600-26871800	Enhancers	Primary B cells from peripheral blood	blood
28	chr4:26864600-26872600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr4:26864600-26885600	Weak transcription	Thymus	Thymus
30	chr4:26864800-26867200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr4:26864800-26868000	Enhancers	HepG2	liver
32	chr4:26864800-26869200	Weak transcription	Fetal Heart	heart
33	chr4:26864800-26869400	Weak transcription	NH-A	brain
34	chr4:26864800-26871200	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr4:26864800-26872600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:26865000-26870600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:26865200-26869400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:26865200-26873000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:26865200-26873200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:26865400-26867000	Weak transcription	Right Atrium	heart
41	chr4:26865400-26867200	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr4:26865400-26869400	Weak transcription	Fetal Muscle Leg	muscle
43	chr4:26865400-26869600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:26865600-26867200	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr4:26865600-26869200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr4:26865600-26869400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr4:26865600-26869400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr4:26865600-26869400	Weak transcription	Fetal Stomach	stomach
49	chr4:26865600-26869800	Enhancers	Brain Angular Gyrus	brain
50	chr4:26865600-26870000	Enhancers	Dnd41	blood

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