Variant report

Variant	rs1402129
Chromosome Location	chr2:50616839-50616840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10182151	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10191436	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10194754	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10865246	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap]
rs11125300	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs11125301	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs11125304	0.82[ASN][1000 genomes]
rs12465806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12622261	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs13382330	0.89[CEU][hapmap]
rs13394447	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1402122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1402126	1.00[CEU][hapmap]
rs1402127	0.82[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1402128	0.89[CEU][hapmap]
rs1402167	0.93[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs1520435	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap]
rs1520450	0.96[CEU][hapmap]
rs1520452	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1520453	1.00[CEU][hapmap]
rs1818713	1.00[CEU][hapmap]
rs1829534	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1851013	0.85[CEU][hapmap]
rs1851014	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1915174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1949569	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1996669	0.84[ASN][1000 genomes]
rs2037387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs2139628	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs2160444	0.82[CEU][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap]
rs2351518	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2351519	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4318425	0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs4377361	0.89[CEU][hapmap]
rs4971669	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4971673	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4971675	0.82[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs6545167	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs6545169	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs6722443	0.92[CEU][hapmap]
rs6728741	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs6728836	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7559624	0.96[CEU][hapmap]
rs7564130	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs7574552	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7577661	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs7587241	0.96[CEU][hapmap];0.92[YRI][hapmap]
rs7599863	0.90[ASN][1000 genomes]
rs7607203	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs883027	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs939399	0.85[CEU][hapmap]
rs939400	0.85[CEU][hapmap]
rs9678669	0.82[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9917332	0.85[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932915	chr2:50306630-50628415	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv492164	chr2:50399251-51029090	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1000653	chr2:50417660-51083470	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv535693	chr2:50417660-51083470	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv948548	chr2:50569117-50695100	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv948361	chr2:50611076-50785178	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1402129	ARHGAP26	cis	Frontal Cortex	GTEx

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

No data

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