Variant report

Variant	rs10225587
Chromosome Location	chr7:126904423-126904424
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10226889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10246314	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10247396	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10250895	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10254695	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10255618	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10269524	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270765	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1111182	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11563673	0.94[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11980484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706771	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13231840	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1582259	0.84[CEU][hapmap]
rs1592377	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17862331	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17862334	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17862337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17863254	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17863259	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17864178	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17867808	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17869568	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1858774	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2097608	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808116	0.95[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs4141414	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes]
rs4141415	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55647740	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55734624	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948480	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6954027	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6965338	0.89[YRI][hapmap]
rs7776557	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.96[EUR][1000 genomes]
rs7792594	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7793635	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.96[EUR][1000 genomes]
rs7793907	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794751	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7797935	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7800526	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs916597	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889189	chr7:126699088-126963028	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv464712	chr7:126881029-126908258	Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv608380	chr7:126881029-126908258	Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10225587	GRM8	cis	parietal	SCAN
rs10225587	PAX4	cis	cerebellum	SCAN
rs10225587	MIR593	cis	lymphoblastoid	seeQTL
rs10225587	FSCN3	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:126899600-126904600	Weak transcription	Gastric	stomach
2	chr7:126904000-126905000	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr7:126904400-126904800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

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