Variant report

Variant	rs17162913
Chromosome Location	chr1:223072278-223072279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223070135..223072909-chr1:223075701..223077307,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10495205	0.82[ASW][hapmap];0.88[YRI][hapmap]
rs12742619	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17163533	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2378609	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2609388	0.94[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap]
rs2609400	0.82[ASW][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.88[YRI][hapmap]
rs2609406	0.94[CHB][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap];0.81[YRI][hapmap]
rs2789966	0.82[ASW][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap]
rs2789967	0.94[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap]
rs2841041	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34202956	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34715037	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35467168	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35681724	0.92[EUR][1000 genomes]
rs35699059	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36133935	0.85[EUR][1000 genomes]
rs61840274	0.97[ASN][1000 genomes]
rs9651262	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv873206	chr1:222985197-223124916	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17162913	TLR5	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223055800-223082800	Weak transcription	Fetal Heart	heart
2	chr1:223065200-223083000	Weak transcription	Aorta	Aorta
3	chr1:223067000-223073000	Weak transcription	Lung	lung
4	chr1:223067200-223077800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:223067400-223072800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:223067800-223072600	Weak transcription	HepG2	liver
7	chr1:223067800-223073000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:223067800-223089400	Weak transcription	Fetal Intestine Small	intestine
9	chr1:223068000-223073000	Weak transcription	Psoas Muscle	Psoas
10	chr1:223068200-223083000	Weak transcription	Fetal Stomach	stomach
11	chr1:223071600-223073800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:223071600-223082800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:223071600-223082800	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:223071600-223083000	Weak transcription	HSMM	muscle
15	chr1:223071600-223089600	Weak transcription	Fetal Muscle Leg	muscle
16	chr1:223071600-223092400	Weak transcription	Ovary	ovary
17	chr1:223071800-223073000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:223071800-223073000	Weak transcription	HSMMtube	muscle
19	chr1:223071800-223082800	Weak transcription	Right Atrium	heart
20	chr1:223071800-223089800	Weak transcription	Fetal Lung	lung

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