Variant report

Variant	rs17519924
Chromosome Location	chr1:58340139-58340140
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	PBX3	chr1:58340021-58340603	SK-N-SH	brain:	n/a	n/a
2	TCF7L2	chr1:58339961-58340416	Hela-S3	cervix:	n/a	n/a
3	PBX3	chr1:58340055-58340530	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr1:58339926-58340446	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
DAB1-AS1	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10889075	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs1101354	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11207128	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs11582953	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs11582988	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes]
rs11587998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12117610	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs12402927	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs17519861	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17579100	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17579464	0.89[GIH][hapmap];1.00[JPT][hapmap]
rs1884486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1936407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2207986	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5014863	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57386386	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61770276	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61770278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61770279	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61770282	0.82[AMR][1000 genomes]
rs61770283	0.83[AMR][1000 genomes]
rs6670853	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6679454	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap]
rs6699475	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs852759	0.87[JPT][hapmap]
rs852771	0.81[GIH][hapmap]
rs852788	0.90[CEU][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs852789	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs852790	0.90[CEU][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs852791	0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs852799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs852800	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv431379	chr1:58224212-58802608	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv829937	chr1:58258288-58406506	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58332200-58340400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:58339200-58340600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:58339600-58340400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:58339600-58340400	Enhancers	NHEK	skin
5	chr1:58339600-58340600	Enhancers	HMEC	breast
6	chr1:58339800-58340400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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