Variant report

Variant	rs7250658
Chromosome Location	chr19:19571100-19571101
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr19:19570940-19571411	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:19570370-19571464	GM12892	blood:	n/a	n/a
3	ELF1	chr19:19570525-19572008	GM12878	blood:	n/a	chr19:19570797-19570810
4	TCF3	chr19:19571070-19571291	GM12878	blood:	n/a	chr19:19571164-19571178
5	POLR2A	chr19:19570975-19571987	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:19570714-19571830	GM15510	blood:	n/a	n/a
7	POLR2A	chr19:19570398-19571981	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:19570465-19571391	GM12892	blood:	n/a	n/a
9	POLR2A	chr19:19570429-19571997	HL-60	blood:	n/a	n/a
10	POLR2A	chr19:19570452-19571384	PFSK-1	brain:	n/a	n/a
11	TCF12	chr19:19571067-19571318	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:19570533-19571967	GM12891	blood:	n/a	n/a
13	POLR2A	chr19:19570496-19571194	K562	blood:	n/a	n/a
14	POLR2A	chr19:19570460-19571362	GM12891	blood:	n/a	n/a
15	POLR2A	chr19:19570317-19571343	HUVEC	blood vessel:	n/a	n/a
16	TCF3	chr19:19570938-19571419	GM12878	blood:	n/a	chr19:19571164-19571178
17	POLR2A	chr19:19570908-19572076	GM12891	blood:	n/a	n/a
18	POLR2A	chr19:19570731-19571463	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:19570319-19571117	U87	brain:	n/a	n/a
20	FOS	chr19:19570006-19571389	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr19:19571064-19571412	GM12891	blood:	n/a	n/a
22	MTA3	chr19:19570204-19572179	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:19570587-19571916	GM18505	blood:	n/a	n/a
24	CEBPB	chr19:19571094-19571451	IMR90	lung:	n/a	n/a
25	POLR2A	chr19:19570948-19571987	K562	blood:	n/a	n/a
26	POLR2A	chr19:19570428-19571117	U87	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19570132..19572642-chr19:19597884..19599709,3	K562	blood:
2	chr19:19524964..19526916-chr19:19569433..19571112,2	MCF-7	breast:
3	chr19:19515119..19517741-chr19:19568755..19571176,2	MCF-7	breast:
4	chr19:19569495..19572698-chr19:19572718..19574339,3	K562	blood:
5	chr19:19570376..19575066-chr19:19577857..19582377,6	K562	blood:
6	chr19:19569916..19571942-chr19:19620244..19622039,2	K562	blood:
7	chr19:19520647..19523347-chr19:19569351..19571784,4	K562	blood:

No data

Variant related genes	Relation type
GATAD2A	TF binding region
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10401193	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10402308	0.81[EUR][1000 genomes]
rs10402451	0.83[ASN][1000 genomes]
rs10402627	0.81[ASN][1000 genomes]
rs10404728	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10405625	0.87[ASN][1000 genomes]
rs10410664	0.87[ASN][1000 genomes]
rs10414830	0.87[ASN][1000 genomes]
rs10419912	0.82[ASN][1000 genomes]
rs1047361	0.83[ASN][1000 genomes]
rs1054284	0.89[ASN][1000 genomes]
rs1063966	0.81[ASN][1000 genomes]
rs11669516	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12972397	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12973258	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12975119	0.87[ASN][1000 genomes]
rs12977524	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12981405	0.87[EUR][1000 genomes]
rs12983940	0.91[AMR][1000 genomes]
rs1465695	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1469712	0.87[ASN][1000 genomes]
rs1469713	0.86[ASN][1000 genomes]
rs17288409	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1808653	0.83[ASN][1000 genomes]
rs1865034	0.83[ASN][1000 genomes]
rs2082421	0.91[ASN][1000 genomes]
rs2099333	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2099334	0.87[ASN][1000 genomes]
rs2163804	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2163805	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2288852	0.83[ASN][1000 genomes]
rs2315610	0.82[ASN][1000 genomes]
rs28478453	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2916073	0.87[ASN][1000 genomes]
rs2916074	0.87[ASN][1000 genomes]
rs2916076	0.87[ASN][1000 genomes]
rs2965182	0.87[ASN][1000 genomes]
rs2965183	0.87[ASN][1000 genomes]
rs2965188	0.81[ASN][1000 genomes]
rs34647936	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3752151	0.89[ASN][1000 genomes]
rs3794990	0.83[ASN][1000 genomes]
rs3794993	0.83[ASN][1000 genomes]
rs4808196	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4808198	0.86[ASN][1000 genomes]
rs4808199	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808200	0.87[ASN][1000 genomes]
rs4808202	0.87[ASN][1000 genomes]
rs4808203	0.87[ASN][1000 genomes]
rs4808950	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4808955	0.87[ASN][1000 genomes]
rs4808957	0.87[ASN][1000 genomes]
rs4808959	0.87[ASN][1000 genomes]
rs4808960	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808961	0.87[ASN][1000 genomes]
rs4808964	0.91[ASN][1000 genomes]
rs60003758	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60321073	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6511036	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6511038	0.81[ASN][1000 genomes]
rs6909	0.81[ASN][1000 genomes]
rs7252888	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7256149	0.89[ASN][1000 genomes]
rs7258508	0.81[EUR][1000 genomes]
rs747050	0.82[ASN][1000 genomes]
rs751856	0.83[ASN][1000 genomes]
rs751858	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs754255	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs892021	0.83[ASN][1000 genomes]
rs892022	0.91[ASN][1000 genomes]
rs9917108	0.86[ASN][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	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7250658	KIAA0892	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19551000-19571200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:19558200-19571400	Weak transcription	Brain Germinal Matrix	brain
3	chr19:19564400-19571800	Weak transcription	Fetal Kidney	kidney
4	chr19:19567000-19573600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:19567000-19575000	Enhancers	Spleen	Spleen
6	chr19:19567000-19576200	Enhancers	Gastric	stomach
7	chr19:19567000-19576600	Genic enhancers	Fetal Intestine Small	intestine
8	chr19:19567200-19576000	Enhancers	Fetal Intestine Large	intestine
9	chr19:19567400-19575000	Enhancers	Small Intestine	intestine
10	chr19:19567800-19571200	Genic enhancers	Dnd41	blood
11	chr19:19568200-19571600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:19568200-19575600	Enhancers	Lung	lung
13	chr19:19568200-19575800	Enhancers	Placenta	Placenta
14	chr19:19568400-19575400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr19:19568600-19571600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr19:19568600-19572600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr19:19568600-19575400	Enhancers	Liver	Liver
18	chr19:19568600-19575400	Enhancers	Psoas Muscle	Psoas
19	chr19:19568600-19575600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:19568600-19575800	Enhancers	Left Ventricle	heart
21	chr19:19568600-19575800	Enhancers	Right Atrium	heart
22	chr19:19568600-19576000	Enhancers	Fetal Lung	lung
23	chr19:19568600-19576200	Enhancers	Stomach Mucosa	stomach
24	chr19:19568600-19576400	Enhancers	Pancreas	Pancrea
25	chr19:19568800-19571600	Enhancers	Brain Anterior Caudate	brain
26	chr19:19568800-19574800	Enhancers	HSMMtube	muscle
27	chr19:19568800-19575000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr19:19568800-19575000	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr19:19569000-19572400	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr19:19569000-19575400	Enhancers	Right Ventricle	heart
31	chr19:19569000-19575800	Enhancers	Esophagus	oesophagus
32	chr19:19569200-19572000	Flanking Active TSS	GM12878-XiMat	blood
33	chr19:19569200-19575600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:19569200-19575800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:19569200-19576200	Weak transcription	Hela-S3	cervix
36	chr19:19569400-19571400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr19:19569400-19571400	Genic enhancers	NHEK	skin
38	chr19:19569400-19571800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:19569400-19572400	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr19:19569400-19572600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:19569400-19572800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr19:19569400-19573800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr19:19569400-19575800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:19569600-19571200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:19569600-19571600	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr19:19569600-19572400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr19:19569600-19572400	Enhancers	Fetal Muscle Trunk	muscle
48	chr19:19569600-19572600	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr19:19569600-19572600	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr19:19569600-19572800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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