Variant report

Variant	rs2163933
Chromosome Location	chr4:21096827-21096828
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10013055	0.88[JPT][hapmap]
rs10022535	0.88[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs10032561	0.82[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap]
rs10034038	0.88[JPT][hapmap]
rs10433822	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516374	0.88[JPT][hapmap]
rs10938831	1.00[ASN][1000 genomes]
rs10938837	0.88[JPT][hapmap]
rs11735843	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735844	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736507	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736572	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11935122	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11944165	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11945600	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap]
rs11945646	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap]
rs11945692	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap]
rs12510687	0.81[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs12639638	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12640310	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12640491	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12642886	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644941	0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12646316	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1364832	0.88[JPT][hapmap];0.90[MEX][hapmap]
rs1364833	0.88[JPT][hapmap]
rs1364838	0.88[JPT][hapmap]
rs1364839	0.88[JPT][hapmap]
rs1368646	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1368648	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17445800	0.88[JPT][hapmap]
rs17446667	0.88[JPT][hapmap]
rs17447922	0.88[JPT][hapmap]
rs17447985	0.88[JPT][hapmap]
rs17448106	0.88[JPT][hapmap]
rs17448392	0.88[JPT][hapmap]
rs17505566	0.83[JPT][hapmap]
rs17506080	0.88[JPT][hapmap]
rs17506108	0.87[JPT][hapmap]
rs17513252	0.88[JPT][hapmap]
rs17574283	0.85[ASN][1000 genomes]
rs17636197	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs17637027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2043387	0.86[EUR][1000 genomes]
rs2043388	0.81[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap]
rs2113966	0.88[JPT][hapmap]
rs2163931	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2163934	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs28406534	0.86[EUR][1000 genomes]
rs2874892	0.87[JPT][hapmap]
rs4572877	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4574407	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs4590029	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4599408	0.88[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs4615170	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap]
rs55737345	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55885656	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55957496	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56025335	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56139613	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56412118	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58548088	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59223154	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59416831	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60444813	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61644618	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810466	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6810897	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6815915	0.84[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6817687	0.93[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs6832569	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6832607	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6835991	0.88[JPT][hapmap]
rs6840528	0.88[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs6845231	0.81[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap]
rs6845961	0.88[JPT][hapmap]
rs6854888	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6855710	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs6858766	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs720852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs720853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs73802481	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7658908	1.00[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	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1013365	chr4:20834054-21609078	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv829878	chr4:20966047-21138626	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv878745	chr4:21054348-21155716	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv878746	chr4:21054348-21169062	Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv878747	chr4:21057794-21169062	Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv522328	chr4:21083553-21096827	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2163933	LCORL	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links