Variant report

Variant	rs56289107
Chromosome Location	chr15:40626978-40626979
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:40625855-40627035	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr15:40626243-40627208	U87	brain:	n/a	n/a
3	POLR2A	chr15:40626941-40627198	U87	brain:	n/a	n/a
4	MAX	chr15:40625932-40627462	NB4	blood:	n/a	n/a
5	POLR2A	chr15:40626243-40627045	U87	brain:	n/a	n/a
6	POLR2A	chr15:40626551-40627066	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr15:40625755-40627147	HUVEC	blood vessel:	n/a	n/a
8	SPI1	chr15:40625955-40627033	GM12878	blood:	n/a	n/a
9	ESR1	chr15:40626975-40627668	T-47D	breast:	n/a	chr15:40627379-40627394
10	SPI1	chr15:40626129-40626989	HL-60	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40626383..40628344-chr15:40677759..40680121,2	K562	blood:
2	chr15:40626473..40628629-chr15:40636681..40638741,2	K562	blood:
3	chr15:40589867..40591704-chr15:40625976..40628292,2	MCF-7	breast:
4	chr15:40619706..40623827-chr15:40624940..40628910,6	MCF-7	breast:
5	chr15:40613279..40619250-chr15:40625286..40632667,13	MCF-7	breast:
6	chr15:40612389..40614304-chr15:40626844..40628895,2	K562	blood:
7	chr15:40625172..40629583-chr15:40631432..40633911,6	MCF-7	breast:
8	chr15:40626926..40627758-chr15:40701393..40702256,3	MCF-7	breast:
9	chr15:40593194..40594991-chr15:40625827..40627495,2	K562	blood:

No data

Variant related genes	Relation type
RNA5SP392	TF binding region
ENSG00000259330	Chromatin interaction
ENSG00000137841	Chromatin interaction
ENSG00000188549	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11540714	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008462	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55945670	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56044352	1.00[ASN][1000 genomes]
rs56232597	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs56289107	IVD	Cis_1M	lymphoblastoid	RTeQTL
rs56289107	KNSTRN	cis	Esophagus Muscularis	GTEx
rs56289107	KNSTRN	cis	Whole Blood	GTEx
rs56289107	KNSTRN	cis	Heart Left Ventricle	GTEx
rs56289107	KNSTRN	cis	Artery Tibial	GTEx
rs56289107	KNSTRN	cis	Artery Aorta	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40617200-40630200	Weak transcription	A549	lung
2	chr15:40617400-40627000	Weak transcription	Gastric	stomach
3	chr15:40618400-40628200	Weak transcription	Brain Germinal Matrix	brain
4	chr15:40619400-40627400	Enhancers	Placenta	Placenta
5	chr15:40619600-40630400	Enhancers	Primary hematopoietic stem cells	blood
6	chr15:40620000-40627800	Enhancers	Left Ventricle	heart
7	chr15:40620400-40628200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:40620800-40629600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:40621000-40627000	Enhancers	HSMMtube	muscle
10	chr15:40621000-40630200	Weak transcription	HepG2	liver
11	chr15:40621000-40637600	Enhancers	Fetal Heart	heart
12	chr15:40621200-40633400	Weak transcription	Fetal Kidney	kidney
13	chr15:40621400-40627000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:40621400-40629800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr15:40621800-40627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:40622400-40633800	Enhancers	Spleen	Spleen
17	chr15:40622800-40628400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:40623000-40629400	Weak transcription	Brain Substantia Nigra	brain
19	chr15:40623000-40630600	Weak transcription	Aorta	Aorta
20	chr15:40623200-40628200	Weak transcription	Brain Anterior Caudate	brain
21	chr15:40623200-40629600	Weak transcription	Ovary	ovary
22	chr15:40623200-40630200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:40623400-40630200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:40623800-40627600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr15:40623800-40630600	Enhancers	Fetal Thymus	thymus
26	chr15:40624200-40630400	Weak transcription	Brain Angular Gyrus	brain
27	chr15:40624200-40630600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:40624600-40627600	Enhancers	Primary T cells from cord blood	blood
29	chr15:40624600-40628600	Enhancers	Right Atrium	heart
30	chr15:40625000-40627200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:40625000-40629600	Genic enhancers	Fetal Muscle Leg	muscle
32	chr15:40625200-40628200	Enhancers	HUVEC	blood vessel
33	chr15:40625400-40627200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr15:40625400-40627400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:40625400-40627600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:40625800-40627000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr15:40625800-40627000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:40625800-40627000	Enhancers	Osteobl	bone
39	chr15:40625800-40627200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr15:40625800-40627200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr15:40625800-40627200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr15:40625800-40627200	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr15:40625800-40627200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:40625800-40627200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr15:40625800-40627200	Enhancers	K562	blood
46	chr15:40625800-40627400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr15:40625800-40627400	Enhancers	Primary B cells from peripheral blood	blood
48	chr15:40625800-40627400	Enhancers	Thymus	Thymus
49	chr15:40625800-40627600	Enhancers	Primary T cells fromperipheralblood	blood
50	chr15:40625800-40627600	Enhancers	Skeletal Muscle Female	skeletal muscle

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