Variant report

Variant	rs2970199
Chromosome Location	chr1:222177454-222177455
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12117316	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12120736	0.87[EUR][1000 genomes]
rs12122410	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12126368	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12129517	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12136244	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12137305	0.87[EUR][1000 genomes]
rs12137800	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12139468	0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[YRI][hapmap];0.91[ASN][1000 genomes]
rs12140406	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1339869	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1339870	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17011253	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2153352	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2185327	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2378497	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2378498	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2378499	0.91[ASN][1000 genomes]
rs2790762	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2800859	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2800860	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3121626	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs5013041	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55756813	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56054113	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56236427	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61823896	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61823902	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61823903	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61823905	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs996854	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014333	chr1:222131785-222245578	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv1009077	chr1:222176979-222180320	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2970199	GPATCH2	cis	parietal	SCAN
rs2970199	IARS2	cis	cerebellum	SCAN
rs2970199	TP53BP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222169200-222184000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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