Variant report

Variant	rs9999056
Chromosome Location	chr4:26880639-26880640
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	CEBPB	chr4:26880556-26881111	Hela-S3	cervix:	n/a	chr4:26880919-26880932 chr4:26880919-26880930 chr4:26880921-26880932 chr4:26880826-26880843 chr4:26880827-26880838
2	FOS	chr4:26880541-26881074	MCF10A-Er-Src	breast:	n/a	chr4:26880722-26880734 chr4:26880772-26880780
3	STAT3	chr4:26880588-26881004	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr4:26880528-26881099	MCF10A-Er-Src	breast:	n/a	n/a
5	SETDB1	chr4:26880196-26880778	U2OS	brain:	n/a	n/a
6	CEBPB	chr4:26880638-26881131	HCT-116	colon:	n/a	chr4:26880919-26880932 chr4:26880919-26880930 chr4:26880921-26880932 chr4:26880826-26880843 chr4:26880827-26880838
7	FOS	chr4:26880562-26881091	MCF10A-Er-Src	breast:	n/a	chr4:26880722-26880734 chr4:26880772-26880780
8	POLR2A	chr4:26880523-26881052	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr4:26880557-26881032	MCF10A-Er-Src	breast:	n/a	n/a
10	CBX3	chr4:26880345-26880863	K562	blood:	n/a	n/a
11	FOS	chr4:26880518-26881072	MCF10A-Er-Src	breast:	n/a	chr4:26880722-26880734 chr4:26880772-26880780
12	CEBPB	chr4:26880582-26881091	IMR90	lung:	n/a	chr4:26880919-26880932 chr4:26880919-26880930 chr4:26880921-26880932 chr4:26880826-26880843 chr4:26880827-26880838
13	MYC	chr4:26880518-26881153	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr4:26880557-26881103	MCF10A-Er-Src	breast:	n/a	chr4:26880722-26880734 chr4:26880772-26880780
15	STAT3	chr4:26880602-26881090	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:26879279..26881991-chr4:26883787..26885649,2	K562	blood:
2	chr4:26860902..26863056-chr4:26879948..26882121,2	K562	blood:
3	chr4:26861238..26864586-chr4:26879222..26882735,4	MCF-7	breast:
4	chr4:26860284..26863900-chr4:26879948..26882544,3	K562	blood:

Variant related genes	Relation type
ENSG00000248340	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]
rs10939139	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11727649	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12505133	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4302449	0.91[EUR][1000 genomes]
rs4586918	0.91[EUR][1000 genomes]
rs55809332	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7667007	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7671671	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7691908	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[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
rs9999056	RP11-293A21.1	cis	Skin Sun Exposed Lower leg	GTEx
rs9999056	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26864400-26886600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr4:26864600-26885600	Weak transcription	Thymus	Thymus
3	chr4:26866000-26881800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:26867200-26884200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:26869800-26886000	Weak transcription	Fetal Stomach	stomach
6	chr4:26870600-26881800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:26870800-26880800	Weak transcription	Stomach Mucosa	stomach
8	chr4:26873000-26886200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr4:26873400-26883600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:26873800-26881200	Weak transcription	Fetal Heart	heart
11	chr4:26873800-26881400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:26875600-26881400	Weak transcription	Right Atrium	heart
13	chr4:26875600-26904600	Weak transcription	Brain Anterior Caudate	brain
14	chr4:26875800-26888200	Weak transcription	Adipose Nuclei	Adipose
15	chr4:26876000-26881400	Weak transcription	Pancreas	Pancrea
16	chr4:26876400-26885600	Weak transcription	Fetal Lung	lung
17	chr4:26877400-26882800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:26878000-26885400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:26878600-26885600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr4:26878600-26885800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr4:26879000-26880800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:26879200-26880800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:26879200-26881800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr4:26879200-26881800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:26879200-26882200	Enhancers	Primary T cells fromperipheralblood	blood
26	chr4:26879200-26882200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr4:26879200-26885400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr4:26879200-26885400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr4:26879400-26882000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr4:26880000-26880800	Enhancers	HMEC	breast
31	chr4:26880000-26881400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr4:26880000-26881800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:26880200-26881400	Weak transcription	Small Intestine	intestine
34	chr4:26880200-26882000	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr4:26880200-26882200	Enhancers	Primary T cells from cord blood	blood
36	chr4:26880200-26884200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:26880200-26885000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr4:26880200-26885000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr4:26880200-26885600	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr4:26880400-26880800	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr4:26880400-26880800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:26880400-26880800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr4:26880400-26881000	Flanking Active TSS	NHEK	skin
44	chr4:26880400-26881600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:26880400-26884000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:26880600-26881000	Weak transcription	Primary B cells from cord blood	blood
47	chr4:26880600-26881000	Active TSS	Liver	Liver
48	chr4:26880600-26881400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:26880600-26881400	Weak transcription	Psoas Muscle	Psoas
50	chr4:26880600-26881400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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