Variant report

Variant	rs10500179
Chromosome Location	chr7:147054730-147054731
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10500187	0.82[MEX][hapmap]
rs10952677	0.82[MEX][hapmap]
rs11769736	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs11772135	0.82[MEX][hapmap]
rs13221003	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs13224292	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs13224673	0.82[MEX][hapmap]
rs13227072	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs13233234	0.82[MEX][hapmap]
rs13236876	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs13247289	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13247402	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1357896	0.88[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs1404711	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs1525227	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17412444	0.88[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs17413110	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs17497254	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs17497557	0.91[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2204412	0.92[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2620485	0.92[YRI][hapmap]
rs34459574	0.93[EUR][1000 genomes]
rs35594861	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35609387	0.93[EUR][1000 genomes]
rs67361115	0.93[EUR][1000 genomes]
rs73473166	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs735261	1.00[JPT][hapmap]
rs7779279	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs7781303	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7785125	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7798078	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7798162	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs7810103	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs826821	0.85[YRI][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	nsv933033	chr7:146720301-147081560	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1033898	chr7:146721499-147081768	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv931005	chr7:146730472-147381257	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1033398	chr7:146989035-147101573	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	n/a
5	nsv465192	chr7:147001077-147086045	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	n/a
6	nsv608943	chr7:147001077-147086045	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10500179	KCNH2	cis	parietal	SCAN
rs10500179	PIP	cis	parietal	SCAN
rs10500179	OR6W1P	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:147052200-147055800	Weak transcription	Brain Hippocampus Middle	brain

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