Variant report

Variant	rs9613617
Chromosome Location	chr22:28847896-28847897
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28847241..28850416-chr22:28850940..28854599,3	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10427676	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10483150	1.00[YRI][hapmap]
rs134527	0.95[JPT][hapmap]
rs134544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17412920	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17504822	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2346395	1.00[MEX][hapmap]
rs5752728	0.88[ASN][1000 genomes]
rs5752729	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs5752745	0.81[CEU][hapmap]
rs5752746	1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs5752766	0.80[EUR][1000 genomes]
rs5762572	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs5762604	0.95[ASN][1000 genomes]
rs5762622	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762654	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762656	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762659	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5762666	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5762686	0.80[CEU][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];0.81[ASN][1000 genomes]
rs5762736	0.81[EUR][1000 genomes]
rs695388	0.90[JPT][hapmap]
rs7286920	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7288416	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73168176	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs738199	0.81[CEU][hapmap]
rs9306454	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs9306455	0.80[ASN][1000 genomes]
rs9306458	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9608677	0.85[MEX][hapmap]
rs9608692	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9613609	0.96[ASN][1000 genomes]
rs9613630	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9613639	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9613658	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1067544	chr22:28755418-29055246	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv544674	chr22:28755418-29055246	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv588880	chr22:28807277-29001789	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9613617	MTFP1	cis	cerebellum	SCAN
rs9613617	SF3A1	cis	cerebellum	SCAN
rs9613617	TTC28	cis	cerebellum	SCAN
rs9613617	C22orf13	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28839800-28861200	Weak transcription	Ovary	ovary
2	chr22:28840000-28849600	Weak transcription	Fetal Brain Male	brain
3	chr22:28842600-28849600	Weak transcription	Psoas Muscle	Psoas
4	chr22:28845400-28850000	Weak transcription	Fetal Brain Female	brain
5	chr22:28846200-28850600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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