Variant report

Variant	rs7288416
Chromosome Location	chr22:28799436-28799437
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10427676	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs134527	0.90[JPT][hapmap]
rs134544	0.94[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs17412920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17504822	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2056962	1.00[ASW][hapmap]
rs2223369	1.00[ASW][hapmap]
rs2346395	1.00[ASW][hapmap];0.85[MEX][hapmap]
rs5752728	0.94[ASN][1000 genomes]
rs5752729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752745	0.85[CEU][hapmap]
rs5752746	0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs5752766	0.91[EUR][1000 genomes]
rs5762532	0.96[CEU][hapmap]
rs5762572	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762604	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762656	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[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];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762659	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5762664	1.00[LWK][hapmap]
rs5762666	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5762686	1.00[ASW][hapmap];0.84[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs5762736	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs695388	0.85[JPT][hapmap]
rs7286920	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73168176	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs738199	0.85[CEU][hapmap]
rs738995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs738996	1.00[ASW][hapmap]
rs9306454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs9306455	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9306458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9608677	1.00[ASW][hapmap]
rs9608692	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9613609	0.98[ASN][1000 genomes]
rs9613617	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]
rs9613630	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]
rs9613639	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9613658	0.91[EUR][1000 genomes];0.81[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7288416	TTC28	cis	cerebellum	SCAN
rs7288416	CABP7	cis	cerebellum	SCAN
rs7288416	TFIP11	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28791400-28800400	Weak transcription	Fetal Muscle Leg	muscle
2	chr22:28792600-28801800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:28792800-28805200	Weak transcription	Fetal Intestine Large	intestine
4	chr22:28793000-28808200	Weak transcription	Aorta	Aorta
5	chr22:28793000-28808600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr22:28793000-28814000	Weak transcription	Left Ventricle	heart
7	chr22:28793000-28819800	Weak transcription	Fetal Intestine Small	intestine
8	chr22:28793400-28806200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr22:28794200-28806000	Weak transcription	NHDF-Ad	bronchial
10	chr22:28794600-28804600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr22:28794600-28804800	Weak transcription	Fetal Stomach	stomach
12	chr22:28794600-28806000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr22:28794600-28806000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr22:28795000-28803400	Weak transcription	Brain Anterior Caudate	brain
15	chr22:28795200-28803200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr22:28796600-28802200	Weak transcription	Fetal Brain Female	brain
17	chr22:28798400-28802600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr22:28798400-28809800	Weak transcription	Fetal Lung	lung
19	chr22:28798600-28803400	Weak transcription	Brain Hippocampus Middle	brain
20	chr22:28798800-28799600	Weak transcription	Fetal Brain Male	brain
21	chr22:28798800-28821200	Weak transcription	Dnd41	blood
22	chr22:28799400-28799600	Enhancers	Psoas Muscle	Psoas

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