Variant report

Variant	rs17151750
Chromosome Location	chr7:25536879-25536880
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10230604	0.94[ASN][1000 genomes]
rs10242326	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10486459	0.94[ASN][1000 genomes]
rs12667972	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12668322	0.96[ASN][1000 genomes]
rs12668343	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12672646	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12673720	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1393675	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17151744	0.97[ASN][1000 genomes]
rs17151747	1.00[ASN][1000 genomes]
rs17151753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151766	0.96[ASN][1000 genomes]
rs17151770	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61238582	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs731007	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs731008	0.80[ASN][1000 genomes]
rs73275511	0.99[ASN][1000 genomes]
rs73275554	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7796244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv606426	chr7:25254125-25621579	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17151750	HOXA9	cis	cerebellum	SCAN
rs17151750	HOXA3	cis	cerebellum	SCAN
rs17151750	CDCA7L	cis	cerebellum	SCAN
rs17151750	CDCA7L	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25532000-25537000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr7:25534400-25537200	Enhancers	Fetal Muscle Leg	muscle
3	chr7:25536000-25537000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr7:25536200-25537000	Weak transcription	Colon Smooth Muscle	Colon
5	chr7:25536200-25537000	Flanking Active TSS	GM12878-XiMat	blood
6	chr7:25536200-25543200	Weak transcription	Fetal Stomach	stomach
7	chr7:25536400-25539000	Weak transcription	Fetal Lung	lung
8	chr7:25536600-25537000	Enhancers	Primary T cells from cord blood	blood
9	chr7:25536600-25537000	Enhancers	Primary hematopoietic stem cells	blood
10	chr7:25536600-25537000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr7:25536800-25537000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr7:25536800-25537000	Enhancers	Adipose Nuclei	Adipose
13	chr7:25536800-25537200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr7:25536800-25537200	Enhancers	Primary B cells from cord blood	blood
15	chr7:25536800-25537200	Enhancers	Primary B cells from peripheral blood	blood
16	chr7:25536800-25537200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr7:25536800-25537200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr7:25536800-25537200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr7:25536800-25537200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr7:25536800-25537200	Enhancers	K562	blood
21	chr7:25536800-25539400	Weak transcription	Ovary	ovary
22	chr7:25536800-25540000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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