Variant report

Variant	rs17456828
Chromosome Location	chr1:57802255-57802256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10493216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493217	0.83[ASN][1000 genomes]
rs11805025	1.00[CHD][hapmap]
rs166552	1.00[CHD][hapmap]
rs17115713	1.00[CHD][hapmap]
rs17422855	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17424237	1.00[ASN][1000 genomes]
rs17424278	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[ASN][1000 genomes]
rs17424691	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[ASN][1000 genomes]
rs17456794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17456884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17458265	1.00[ASN][1000 genomes]
rs267644	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs41324751	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[ASN][1000 genomes]
rs545796	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs56111567	1.00[ASN][1000 genomes]
rs561221	1.00[CHB][hapmap]
rs56168067	1.00[ASN][1000 genomes]
rs56221416	1.00[ASN][1000 genomes]
rs655672	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6693181	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72674849	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72674850	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72674851	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72674853	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72674856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539971	1.00[CHB][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	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv871943	chr1:57784144-57855876	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv871530	chr1:57793948-57858319	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17456828	USP24	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57792400-57806200	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57800000-57826600	Weak transcription	Left Ventricle	heart
3	chr1:57801200-57803200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:57801600-57803800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:57801800-57803200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:57802000-57803200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr1:57802000-57803800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr1:57802200-57802400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:57802200-57802600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:57802200-57802600	Enhancers	Fetal Lung	lung
11	chr1:57802200-57803000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:57802200-57803200	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:57802200-57803400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:57802200-57803400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr1:57802200-57809000	Weak transcription	Fetal Brain Male	brain

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