Variant report

Variant	rs17096897
Chromosome Location	chr1:59379043-59379044
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59377762..59379375-chr1:59386818..59388727,2	K562	blood:
2	chr1:59379022..59379522-chr11:65270691..65271192,2	Hela-S3	cervix:
3	chr1:59377084..59380234-chr1:59380830..59384528,3	K562	blood:
4	chr1:59365659..59367179-chr1:59378330..59379846,2	K562	blood:
5	chr1:59245774..59250120-chr1:59377925..59380159,4	K562	blood:
6	chr1:59246784..59250688-chr1:59376350..59380858,6	K562	blood:

Variant related genes	Relation type
ENSG00000177606	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12071047	0.85[EUR][1000 genomes]
rs12089816	0.85[EUR][1000 genomes]
rs12093908	0.87[EUR][1000 genomes]
rs17118423	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17118441	0.85[EUR][1000 genomes]
rs1886744	1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2011623	0.89[MEX][hapmap]
rs2764908	0.89[MEX][hapmap]
rs2764909	1.00[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs2999129	0.89[MEX][hapmap]
rs35393496	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55675910	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55834295	0.94[EUR][1000 genomes]
rs55872264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56175432	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56219110	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56251271	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56349902	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681035	0.81[MEX][hapmap]
rs72678885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72678896	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72678899	0.92[EUR][1000 genomes]
rs72678900	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72678901	0.92[EUR][1000 genomes]
rs72680106	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72680107	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72680109	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72680113	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72921571	0.89[EUR][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	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv546316	chr1:59368947-59457815	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17096897	NFIA	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59369800-59388200	Weak transcription	Gastric	stomach
2	chr1:59374200-59379800	Enhancers	Fetal Intestine Large	intestine
3	chr1:59374400-59379800	Enhancers	Fetal Intestine Small	intestine
4	chr1:59375800-59379400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:59375800-59380600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:59376400-59379200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:59377800-59382600	Weak transcription	Placenta Amnion	Placenta Amnion

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