Variant report

Variant	rs688898
Chromosome Location	chr3:109642605-109642606
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1164205	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1164206	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2693621	0.88[ASN][1000 genomes]
rs2693634	0.87[ASN][1000 genomes]
rs2700237	0.87[ASN][1000 genomes]
rs2950151	0.87[ASN][1000 genomes]
rs2950152	0.87[ASN][1000 genomes]
rs34825682	0.81[ASN][1000 genomes]
rs581999	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs582946	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs586783	0.82[EUR][1000 genomes]
rs591010	0.89[ASN][1000 genomes]
rs591350	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs593904	0.87[ASN][1000 genomes]
rs595732	0.87[ASN][1000 genomes]
rs598795	0.87[ASN][1000 genomes]
rs598837	0.87[ASN][1000 genomes]
rs599684	0.87[ASN][1000 genomes]
rs600581	0.87[ASN][1000 genomes]
rs600604	0.87[ASN][1000 genomes]
rs601036	0.87[ASN][1000 genomes]
rs601561	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs604088	0.88[ASN][1000 genomes]
rs605795	0.95[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs607043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs607450	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs610419	0.87[ASN][1000 genomes]
rs614845	0.87[ASN][1000 genomes]
rs617480	0.89[ASN][1000 genomes]
rs619279	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs620727	0.89[ASN][1000 genomes]
rs636972	0.87[ASN][1000 genomes]
rs638718	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs642142	0.87[ASN][1000 genomes]
rs649118	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs652762	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs652972	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs655376	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs656615	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs656888	0.85[ASN][1000 genomes]
rs662181	0.87[ASN][1000 genomes]
rs662417	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs666016	0.88[ASN][1000 genomes]
rs667006	0.87[ASN][1000 genomes]
rs671520	0.87[ASN][1000 genomes]
rs686100	0.87[ASN][1000 genomes]
rs686694	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs687239	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs687619	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs687962	0.87[ASN][1000 genomes]
rs689213	0.87[ASN][1000 genomes]
rs776343	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs776344	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009075	chr3:109462019-109800029	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv591270	chr3:109462400-109793785	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv877332	chr3:109575764-110186611	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1009550	chr3:109577315-109795453	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1839660	chr3:109591203-109678542	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv829666	chr3:109593745-109768652	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2754434	chr3:109604310-109777310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv236806	chr3:109638554-109647641	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:109637400-109645200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:109640600-109644400	Enhancers	A549	lung
3	chr3:109640800-109646000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:109641000-109645200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:109641200-109643600	Enhancers	Hela-S3	cervix
6	chr3:109641600-109644200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:109641600-109646600	Weak transcription	HSMM	muscle
8	chr3:109642000-109643000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:109642000-109643400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:109642400-109643000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:109642400-109643000	Enhancers	Fetal Lung	lung
12	chr3:109642400-109643200	Enhancers	HMEC	breast
13	chr3:109642400-109644200	Enhancers	NHEK	skin
14	chr3:109642600-109644400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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