Variant report

Variant	rs338047
Chromosome Location	chr4:173448399-173448400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10006633	1.00[MEX][hapmap]
rs11132947	0.94[EUR][1000 genomes]
rs11939125	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103453	0.95[CEU][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13107068	0.86[EUR][1000 genomes]
rs13113495	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13118772	0.90[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs13122643	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13142236	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13146091	0.90[GIH][hapmap];0.92[TSI][hapmap]
rs13146384	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs13150574	0.84[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs1455122	0.90[CEU][hapmap]
rs1455123	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1551446	0.87[ASW][hapmap];0.95[CEU][hapmap];0.90[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap]
rs17233636	0.95[CEU][hapmap]
rs2085207	0.90[CEU][hapmap]
rs2124204	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap]
rs2332516	0.87[ASW][hapmap];0.95[CEU][hapmap];0.90[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap]
rs337981	0.85[CEU][hapmap]
rs337994	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338005	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs338048	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs338049	0.96[YRI][hapmap]
rs338052	0.95[CEU][hapmap];0.83[YRI][hapmap]
rs338054	0.94[CEU][hapmap];0.85[YRI][hapmap]
rs338055	1.00[CHD][hapmap]
rs338056	0.95[CEU][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs538624	0.95[CEU][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6812783	0.94[CEU][hapmap]
rs7656178	0.95[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7659363	0.90[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669065	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686403	0.95[CEU][hapmap]
rs7686995	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7694525	0.95[CEU][hapmap]

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	nsv1031592	chr4:173112542-173662991	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv537359	chr4:173112542-173662991	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534293	chr4:173121379-173606082	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1031327	chr4:173306405-173465248	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv948856	chr4:173388217-173967546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv4607	chr4:173406293-173457588	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1023134	chr4:173412218-173455427	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1021404	chr4:173413885-173458833	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs338047	GALNTL6	cis	cerebellum	SCAN
rs338047	WDR17	cis	cerebellum	SCAN

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

No data

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