Variant report

Variant	rs2160929
Chromosome Location	chr2:53881872-53881873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10188142	0.81[CHB][hapmap]
rs10490471	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11125515	0.96[ASN][1000 genomes]
rs11682721	0.96[ASN][1000 genomes]
rs11684084	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11889094	0.94[ASN][1000 genomes]
rs11896043	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11902691	0.94[ASN][1000 genomes]
rs12611475	0.92[ASN][1000 genomes]
rs12620583	0.96[ASN][1000 genomes]
rs13414216	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13432632	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs2080715	0.97[ASN][1000 genomes]
rs2111622	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2111623	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2111851	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2160930	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2160931	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2193682	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2193683	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2357693	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2542584	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2542585	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2542588	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2692531	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2692532	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2692536	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2949812	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs3770403	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3770405	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3770406	0.82[CEU][hapmap]
rs3821081	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4671529	0.82[ASN][1000 genomes]
rs4671583	0.82[CHB][hapmap]
rs56081372	0.89[ASN][1000 genomes]
rs56291505	0.95[ASN][1000 genomes]
rs62139772	0.92[ASN][1000 genomes]
rs62139780	0.95[ASN][1000 genomes]
rs62139783	0.97[ASN][1000 genomes]
rs62139835	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6708095	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs6713107	0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs6714891	0.95[ASN][1000 genomes]
rs6727876	0.97[ASN][1000 genomes]
rs6728355	0.95[ASN][1000 genomes]
rs6741239	0.94[ASN][1000 genomes]
rs6743627	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6757393	0.92[ASN][1000 genomes]
rs7556791	0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs7557799	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7557898	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7563054	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs7573991	0.80[ASN][1000 genomes]
rs7584474	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7587217	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7596349	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs7601692	0.85[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs805438	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs805439	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs918207	0.81[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	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv874147	chr2:53772561-53886799	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv984439	chr2:53861720-53955437	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2160929	ACYP2	cis	Muscle Skeletal	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53874200-53935000	Weak transcription	Pancreas	Pancrea
2	chr2:53879400-53895600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:53880400-53882200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:53880600-53882600	Enhancers	Colon Smooth Muscle	Colon
5	chr2:53880600-53883000	Enhancers	Rectal Smooth Muscle	rectum
6	chr2:53881200-53883200	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr2:53881200-53895800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:53881400-53882200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:53881400-53934400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:53881800-53896400	Weak transcription	Aorta	Aorta

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