Variant report

Variant	rs7656954
Chromosome Location	chr4:90784670-90784671
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:90784232..90787122-chr4:90789554..90792365,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10001067	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10004413	0.89[EUR][1000 genomes]
rs10005233	0.83[MEX][hapmap]
rs10028246	0.84[EUR][1000 genomes]
rs12331318	0.88[EUR][1000 genomes]
rs1348224	0.85[EUR][1000 genomes]
rs1372507	0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs1372521	0.84[EUR][1000 genomes]
rs1372522	0.84[EUR][1000 genomes]
rs1442129	0.85[CHD][hapmap]
rs1442134	0.89[CEU][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1442135	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1442140	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1471483	0.87[MEX][hapmap]
rs1822217	0.82[EUR][1000 genomes]
rs1899389	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2011543	0.81[ASN][1000 genomes]
rs2301134	0.92[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2301135	0.83[EUR][1000 genomes]
rs2736994	1.00[ASN][1000 genomes]
rs28403500	0.89[EUR][1000 genomes]
rs28415623	0.84[EUR][1000 genomes]
rs28507349	0.84[EUR][1000 genomes]
rs28734152	0.88[EUR][1000 genomes]
rs28777703	0.89[EUR][1000 genomes]
rs35424815	0.88[EUR][1000 genomes]
rs3756059	0.89[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs3756063	0.83[EUR][1000 genomes]
rs3806789	0.84[EUR][1000 genomes]
rs58864428	0.84[EUR][1000 genomes]
rs6532192	0.85[EUR][1000 genomes]
rs6532193	0.85[EUR][1000 genomes]
rs6532198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6812192	0.89[CEU][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6816736	0.84[EUR][1000 genomes]
rs6817001	0.84[EUR][1000 genomes]
rs6831847	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839608	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6843084	0.84[EUR][1000 genomes]
rs6848181	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs763443	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7671549	0.89[EUR][1000 genomes]
rs7672979	0.88[EUR][1000 genomes]
rs7680557	0.85[EUR][1000 genomes]
rs7680761	0.85[EUR][1000 genomes]
rs7681154	0.85[EUR][1000 genomes]
rs7681440	0.83[MEX][hapmap];0.80[TSI][hapmap]
rs7687945	0.85[EUR][1000 genomes]
rs7691487	0.86[ASN][1000 genomes]
rs7698219	0.89[EUR][1000 genomes]
rs894280	0.85[EUR][1000 genomes]
rs9307077	0.89[CHD][hapmap];0.92[JPT][hapmap];0.86[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	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7656954	FAM190A	cis	cerebellum	SCAN
rs7656954	DSPP	cis	cerebellum	SCAN
rs7656954	SNCA	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90784200-90785000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr4:90784400-90785400	Enhancers	Primary hematopoietic stem cells	blood
3	chr4:90784600-90785000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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