Variant report

Variant	rs2609907
Chromosome Location	chr19:44817865-44817866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1233430	1.00[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1233431	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1233432	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1233433	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1233434	0.93[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs1233436	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1233438	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1233442	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233443	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1233445	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233446	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1233449	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233450	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1233451	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233452	1.00[GIH][hapmap];0.90[TSI][hapmap]
rs1233453	1.00[GIH][hapmap];0.91[TSI][hapmap]
rs1233457	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1233458	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233460	1.00[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233461	1.00[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233462	1.00[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233469	1.00[GIH][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes]
rs1233472	0.81[AMR][1000 genomes]
rs1233474	1.00[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs1234839	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1235163	1.00[GIH][hapmap];0.91[TSI][hapmap]
rs1237178	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1237179	1.00[GIH][hapmap];0.86[TSI][hapmap]
rs1238786	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1347349	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1369100	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1836273	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2164112	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2164113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2168990	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2196185	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2249402	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2262860	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2446491	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2466421	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2571100	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2571105	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2571106	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609883	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609886	1.00[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2609887	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609889	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2609890	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609898	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609905	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2609906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609909	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2722707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722708	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722711	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722716	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722717	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722718	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2722719	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2722721	1.00[CHD][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2722735	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2722736	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2722738	0.89[ASN][1000 genomes]
rs2722739	0.84[ASN][1000 genomes]
rs59555311	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509153	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs874187	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898175	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898176	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898177	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898179	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs984116	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[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	esv3318935	chr19:44813543-44819319	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	esv3318936	chr19:44813543-44819319	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3330033	chr19:44813552-44819322	Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2609907	ZNF473	cis	cerebellum	SCAN
rs2609907	SYT3	cis	cerebellum	SCAN
rs2609907	FLT3LG	cis	parietal	SCAN
rs2609907	ZFP112	trans	cerebellum	SCAN
rs2609907	SNORD33	cis	cerebellum	SCAN
rs2609907	ZNF229	trans	cerebellum	SCAN
rs2609907	GPR77	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44814600-44824600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr19:44817000-44818400	Enhancers	Primary B cells from peripheral blood	blood

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