Variant report

Variant	rs9306454
Chromosome Location	chr22:28663405-28663406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10427676	0.83[EUR][1000 genomes]
rs134527	0.89[JPT][hapmap]
rs134544	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs17412920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs2056962	1.00[ASW][hapmap]
rs2223369	1.00[ASW][hapmap]
rs2346395	1.00[ASW][hapmap];0.85[MEX][hapmap]
rs28865637	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55916256	0.85[ASN][1000 genomes]
rs5752729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs5752745	0.85[CEU][hapmap]
rs5752746	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs5762532	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs5762572	0.84[EUR][1000 genomes]
rs5762622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs695388	0.95[JPT][hapmap]
rs7288416	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]
rs738199	0.85[CEU][hapmap]
rs738995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs738996	1.00[ASW][hapmap]
rs9306455	0.83[EUR][1000 genomes]
rs9608667	0.92[CEU][hapmap]
rs9608677	1.00[ASW][hapmap]
rs9613570	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs9613617	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]

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	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9306454	CABP7	cis	cerebellum	SCAN
rs9306454	TFIP11	cis	cerebellum	SCAN
rs9306454	TTC28	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28646000-28664000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr22:28651800-28690600	Weak transcription	Dnd41	blood
3	chr22:28653000-28664200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr22:28653000-28665000	Weak transcription	Fetal Muscle Leg	muscle
5	chr22:28653000-28671600	Weak transcription	Fetal Stomach	stomach
6	chr22:28656800-28666000	Weak transcription	Small Intestine	intestine
7	chr22:28657000-28664200	Weak transcription	Brain Angular Gyrus	brain
8	chr22:28657000-28691600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr22:28657200-28664000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr22:28659400-28671200	Weak transcription	Fetal Lung	lung
11	chr22:28661400-28664000	Weak transcription	Aorta	Aorta
12	chr22:28662400-28665400	Enhancers	Psoas Muscle	Psoas
13	chr22:28662400-28665800	Enhancers	Adipose Nuclei	Adipose
14	chr22:28662400-28666200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr22:28662600-28665400	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr22:28662800-28663800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr22:28662800-28664200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr22:28662800-28666200	Enhancers	Colon Smooth Muscle	Colon
19	chr22:28662800-28671200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr22:28662800-28671200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr22:28663000-28665400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr22:28663000-28671000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr22:28663200-28663600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr22:28663400-28664400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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