Variant report

Variant	rs4954923
Chromosome Location	chr2:142527100-142527101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1008830	0.86[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10165118	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10193397	1.00[CHB][hapmap]
rs10195141	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496897	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs10928123	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs12474491	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs12474567	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12612082	0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12612242	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12616665	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12616779	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12990449	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13034371	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13412865	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs1567305	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1567306	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1567307	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1567308	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16847091	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16847244	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs16847247	0.95[CHB][hapmap]
rs1866025	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866026	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs1866027	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2009269	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2009270	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048206	0.85[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2118274	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2164697	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2164699	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2217964	0.90[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap]
rs2217965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2890600	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34474362	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34527764	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3856362	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4352182	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4622655	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6759610	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7425972	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs972485	0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs974973	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834394	chr2:142430225-142593264	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv530398	chr2:142474842-142843839	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv459663	chr2:142509570-142568465	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv583236	chr2:142509570-142568465	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	nsv1004379	chr2:142514657-142547597	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv875246	chr2:142527100-142568465	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
7	nsv875247	chr2:142527100-142569099	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
8	nsv875248	chr2:142527100-142572590	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
9	nsv875249	chr2:142527100-142614345	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142525000-142527200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr2:142525000-142530200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr2:142525400-142527200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:142525400-142528000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:142526200-142527200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:142527000-142527400	Enhancers	H9 Cell Line	embryonic stem cell
7	chr2:142527000-142527800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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