Variant report

Variant	rs246965
Chromosome Location	chr5:118890915-118890916
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10042168	0.82[CHB][hapmap]
rs10045066	0.82[CHB][hapmap]
rs10051019	0.83[CHB][hapmap]
rs10069875	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs10073818	0.82[CHB][hapmap]
rs10078097	0.83[CHB][hapmap]
rs10478426	0.83[CHB][hapmap]
rs11241506	0.81[CHB][hapmap]
rs12653056	0.83[CHB][hapmap]
rs12653702	0.83[CHB][hapmap]
rs13361193	0.83[CHB][hapmap]
rs165995	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs2075698	0.83[CHB][hapmap]
rs2257900	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2257901	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2259347	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs2287712	0.83[CHB][hapmap]
rs2303003	0.83[CHB][hapmap]
rs2451816	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2459726	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs246967	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2546210	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs25640	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap]
rs257970	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs257971	0.85[ASN][1000 genomes]
rs257972	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs257973	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs257974	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs257976	0.80[AMR][1000 genomes]
rs26180	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs26181	0.96[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs26184	0.96[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2636961	0.92[CEU][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2636962	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2636964	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2636968	0.96[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2678074	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2678076	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2678091	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs27938	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2945327	0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs32659	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs32662	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.85[ASN][1000 genomes]
rs32663	0.85[ASN][1000 genomes]
rs32664	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs32665	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs35235684	0.88[ASN][1000 genomes]
rs3797363	0.83[CHB][hapmap]
rs3797367	0.82[CHB][hapmap]
rs382719	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3850200	0.83[CHB][hapmap]
rs3850202	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs39970	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs422297	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs426899	0.84[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes]
rs455949	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs457106	0.87[CHB][hapmap]
rs460274	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs461108	0.86[CHB][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap]
rs463098	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs465091	0.91[CHB][hapmap]
rs4895372	0.91[CHB][hapmap]
rs6875595	0.86[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap]
rs6894991	0.83[CHB][hapmap]
rs6895345	0.83[CHB][hapmap]
rs7721602	0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.91[MEX][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	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1016271	chr5:118836891-119487982	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv882776	chr5:118859546-118915408	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv882777	chr5:118870452-118981480	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs246965	SNX24	cis	parietal	SCAN
rs246965	PRR16	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118879000-118891200	Weak transcription	Pancreas	Pancrea
2	chr5:118879200-118892200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:118890600-118891200	Weak transcription	Brain Anterior Caudate	brain
4	chr5:118890600-118896200	Weak transcription	Brain Angular Gyrus	brain

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