Variant report

Variant	rs9613630
Chromosome Location	chr22:28871570-28871571
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10427676	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs134527	0.90[JPT][hapmap]
rs134544	0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs17412920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17504822	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2056962	1.00[ASW][hapmap]
rs2346395	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs5752728	0.89[ASN][1000 genomes]
rs5752729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5752745	0.85[CEU][hapmap]
rs5752746	0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs5752766	0.90[EUR][1000 genomes]
rs5762572	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5762604	0.94[ASN][1000 genomes]
rs5762622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762656	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762659	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5762664	1.00[LWK][hapmap]
rs5762666	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762686	1.00[ASW][hapmap];0.84[CEU][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs5762736	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5762737	0.81[CEU][hapmap]
rs695388	0.85[JPT][hapmap]
rs7286920	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7288416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73168176	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs738199	0.85[CEU][hapmap]
rs9306455	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9306458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9608677	1.00[ASW][hapmap];0.85[MEX][hapmap]
rs9608692	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9613609	0.94[ASN][1000 genomes]
rs9613617	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	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9613658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9613630	C22orf13	cis	parietal	SCAN
rs9613630	MTFP1	cis	cerebellum	SCAN
rs9613630	CABP7	cis	cerebellum	SCAN
rs9613630	TTC28	cis	cerebellum	SCAN
rs9613630	TFIP11	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28861400-28875800	Weak transcription	Fetal Muscle Leg	muscle
2	chr22:28861600-28880200	Weak transcription	Ovary	ovary
3	chr22:28862800-28874800	Weak transcription	Fetal Brain Female	brain
4	chr22:28867800-28873600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:28869000-28873600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr22:28870800-28874800	Weak transcription	Dnd41	blood
7	chr22:28871200-28871600	ZNF genes & repeats	Fetal Intestine Small	intestine

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