Variant report

Variant	rs12593920
Chromosome Location	chr15:41848796-41848797
allele	A/G
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	chr15:41847460-41849421	K562	blood:	n/a	n/a
2	SPI1	chr15:41848788-41849205	HL-60	blood:	n/a	n/a
3	SPI1	chr15:41848787-41849201	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:41847317..41853712-chr15:41951201..41955578,8	K562	blood:
2	chr15:41845325..41848797-chr15:41849286..41852428,6	MCF-7	breast:
3	chr15:41784400..41789772-chr15:41847283..41854059,7	K562	blood:

Variant related genes	Relation type
TYRO3	TF binding region
TCEB1P2	TF binding region
ENSG00000137825	Chromatin interaction
ENSG00000092445	Chromatin interaction
ENSG00000174197	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2277536	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2289743	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28657602	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4924559	0.81[EUR][1000 genomes]
rs6493004	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6493005	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984058	chr15:41848218-41850246	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12593920	MGA	Cis_1M	lymphoblastoid	RTeQTL
rs12593920	LTK	cis	lung	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41837200-41850000	Weak transcription	Brain Anterior Caudate	brain
2	chr15:41837200-41850200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:41845800-41850600	Enhancers	HUVEC	blood vessel
4	chr15:41846000-41850000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr15:41846200-41850000	Weak transcription	Osteobl	bone
6	chr15:41846400-41850000	Weak transcription	HSMMtube	muscle
7	chr15:41847000-41850000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:41847000-41850000	Weak transcription	Left Ventricle	heart
9	chr15:41847200-41849600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:41847200-41850000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr15:41847200-41850000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:41847200-41850000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr15:41847200-41850000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:41847200-41850000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr15:41847400-41849600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:41847400-41849800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:41847400-41850000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:41847400-41850000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr15:41847400-41850000	Weak transcription	Fetal Kidney	kidney
20	chr15:41847400-41850000	Weak transcription	Placenta	Placenta
21	chr15:41847400-41850000	Weak transcription	HSMM	muscle
22	chr15:41847600-41850000	Weak transcription	Brain Angular Gyrus	brain
23	chr15:41847600-41850000	Weak transcription	Fetal Intestine Large	intestine
24	chr15:41847600-41850000	Weak transcription	Fetal Intestine Small	intestine
25	chr15:41847600-41850000	Weak transcription	Spleen	Spleen
26	chr15:41848200-41848800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:41848200-41849000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:41848200-41849400	Enhancers	K562	blood
29	chr15:41848200-41850400	Enhancers	Primary B cells from peripheral blood	blood
30	chr15:41848400-41848800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:41848400-41848800	Enhancers	Right Atrium	heart
32	chr15:41848400-41850000	Weak transcription	Psoas Muscle	Psoas
33	chr15:41848600-41849000	Weak transcription	Adipose Nuclei	Adipose
34	chr15:41848600-41849200	Enhancers	Primary B cells from cord blood	blood

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