Variant report

Variant	rs17113799
Chromosome Location	chr1:56844652-56844653
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	GATA2	chr1:56843907-56844882	SH-SY5Y	brain:	n/a	chr1:56844507-56844516
2	GATA3	chr1:56843985-56844710	SK-N-SH	brain:	n/a	chr1:56844507-56844516
3	RAD21	chr1:56839169-56846366	SK-N-SH	brain:	n/a	chr1:56839904-56839918 chr1:56840249-56840261
4	GATA3	chr1:56844107-56844782	SH-SY5Y	brain:	n/a	chr1:56844507-56844516
5	EP300	chr1:56839159-56845078	SK-N-SH	brain:	n/a	chr1:56842588-56842595 chr1:56841267-56841281

Variant related genes	Relation type
ENSG00000223307	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11206793	0.93[EUR][1000 genomes]
rs11206801	0.84[EUR][1000 genomes]
rs11206802	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12064446	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12067784	0.82[EUR][1000 genomes]
rs12067824	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12090289	0.82[EUR][1000 genomes]
rs12097108	0.82[EUR][1000 genomes]
rs12563026	0.82[EUR][1000 genomes]
rs12567265	0.81[EUR][1000 genomes]
rs17113792	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17113795	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28445007	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28631406	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4269809	0.83[EUR][1000 genomes]
rs4353140	0.83[EUR][1000 genomes]
rs4373790	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4431886	0.83[EUR][1000 genomes]
rs6690394	0.84[EUR][1000 genomes]
rs72662217	0.82[EUR][1000 genomes]
rs7539724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546727	0.83[EUR][1000 genomes]
rs7553068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56839000-56845000	Enhancers	Fetal Muscle Leg	muscle
2	chr1:56839200-56846800	Enhancers	Fetal Stomach	stomach
3	chr1:56839400-56844800	Enhancers	Rectal Smooth Muscle	rectum
4	chr1:56839600-56844800	Enhancers	Colon Smooth Muscle	Colon
5	chr1:56840000-56844800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:56840000-56862400	Weak transcription	Gastric	stomach
7	chr1:56840200-56845000	Enhancers	Brain Germinal Matrix	brain
8	chr1:56842400-56844800	Enhancers	Brain Substantia Nigra	brain
9	chr1:56842400-56862400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:56842600-56844800	Enhancers	Brain Hippocampus Middle	brain
11	chr1:56842600-56849800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:56842600-56850600	Weak transcription	NHDF-Ad	bronchial
13	chr1:56842600-56859800	Weak transcription	Right Ventricle	heart
14	chr1:56842800-56848800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:56843000-56861800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:56843400-56844800	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr1:56843600-56846400	Weak transcription	Right Atrium	heart
18	chr1:56843800-56846000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:56843800-56846000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:56844000-56855800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:56844200-56857800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:56844400-56845200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:56844400-56845400	Enhancers	HepG2	liver
24	chr1:56844600-56844800	Enhancers	Fetal Kidney	kidney
25	chr1:56844600-56846000	Weak transcription	Fetal Lung	lung
26	chr1:56844600-56853000	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links