Variant report

Variant	rs3918467
Chromosome Location	chr6:88180388-88180389
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1051131	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1051148	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10755484	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs13193380	0.80[EUR][1000 genomes]
rs13214153	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs2103764	0.87[ASN][1000 genomes]
rs2207144	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.86[ASN][1000 genomes]
rs2207146	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2268993	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2268994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2273129	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284908	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2300906	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2300909	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2325064	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3757368	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3934838	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4334949	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap]
rs4464759	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap]
rs448580	0.81[MEX][hapmap]
rs4587138	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4587143	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4707373	0.80[EUR][1000 genomes]
rs4707374	0.82[EUR][1000 genomes]
rs6454630	0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6454631	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6454632	0.84[EUR][1000 genomes]
rs6905947	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs6906769	0.84[EUR][1000 genomes]
rs6912958	0.82[ASN][1000 genomes]
rs6914299	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs6916732	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs6923230	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6933587	0.95[CHB][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7741825	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7742965	0.80[EUR][1000 genomes]
rs7754350	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7757636	0.81[EUR][1000 genomes]
rs7761814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7762864	0.84[EUR][1000 genomes]
rs7773906	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs9294379	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs9294381	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs9444504	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444512	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9444519	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs9444522	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs9450688	0.87[ASN][1000 genomes]
rs9450701	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450712	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450723	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9450732	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs9450733	0.83[EUR][1000 genomes]
rs9450752	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap]
rs985764	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3918467	C6orf162	cis	cerebellum	SCAN
rs3918467	SLC35A1	cis	multi-tissue	Pritchard
rs3918467	C6orf166	Cis_1M	lymphoblastoid	RTeQTL
rs3918467	SLC35A1	cis	parietal	SCAN
rs3918467	SLC35A1	cis	lymphoblastoid	seeQTL
rs3918467	C6orf162	cis	parietal	SCAN
rs3918467	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs3918467	SNORD50A	cis	cerebellum	SCAN
rs3918467	C6orf162	Cis_1M	lymphoblastoid	RTeQTL

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

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

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