Variant report

Variant	rs1642884
Chromosome Location	chr7:78556213-78556214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10277798	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs1073416	0.83[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs12705860	0.83[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs1624161	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs1625020	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1642888	0.91[CEU][hapmap];0.80[GIH][hapmap];0.93[TSI][hapmap]
rs1642911	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17151659	0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs17151674	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17505	0.91[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs1799003	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1799004	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1799006	0.91[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs1799021	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs1799022	0.91[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2052403	1.00[CEU][hapmap]
rs2078428	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs6943858	0.94[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs6948152	0.94[CHB][hapmap]
rs7797351	0.91[CEU][hapmap];0.93[TSI][hapmap]
rs7799287	0.91[CEU][hapmap];0.80[GIH][hapmap];0.93[TSI][hapmap]
rs987436	0.83[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs993014	0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464598	chr7:78492642-79483480	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv607659	chr7:78492642-79483480	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv482826	chr7:78548319-78717605	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv471642	chr7:78548320-78717605	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1642884	GNAI1	cis	parietal	SCAN
rs1642884	PCLO	cis	cerebellum	SCAN

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

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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