Variant report

Variant	rs9608677
Chromosome Location	chr22:28741745-28741746
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11703980	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17412920	1.00[ASW][hapmap];0.85[MEX][hapmap]
rs17502181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2056962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs2223369	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs2346395	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs5762656	1.00[ASW][hapmap];0.85[MEX][hapmap]
rs7288416	1.00[ASW][hapmap]
rs73170603	0.87[AFR][1000 genomes]
rs738996	1.00[ASW][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs9306454	1.00[ASW][hapmap]
rs9613574	1.00[CEU][hapmap]
rs9613580	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs9613581	0.91[EUR][1000 genomes]
rs9613588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9613617	0.85[MEX][hapmap]
rs9613630	1.00[ASW][hapmap];0.85[MEX][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9608677	TTC28	cis	cerebellum	SCAN
rs9608677	ZNF251	trans	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28736000-28744200	Weak transcription	Lung	lung
2	chr22:28736400-28746600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr22:28737200-28742200	Weak transcription	Fetal Brain Female	brain
4	chr22:28737200-28742600	Weak transcription	Dnd41	blood
5	chr22:28737200-28747200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr22:28737400-28744000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr22:28737800-28744800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr22:28738000-28751600	Weak transcription	Left Ventricle	heart
9	chr22:28738800-28744200	Weak transcription	Fetal Brain Male	brain
10	chr22:28739600-28741800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr22:28739600-28741800	Enhancers	HMEC	breast
12	chr22:28739600-28741800	Enhancers	NHEK	skin
13	chr22:28740200-28742400	Enhancers	Colon Smooth Muscle	Colon
14	chr22:28740200-28743000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr22:28740600-28741800	Enhancers	Osteobl	bone
16	chr22:28740800-28741800	Enhancers	Fetal Lung	lung
17	chr22:28740800-28741800	Enhancers	NHLF	lung
18	chr22:28740800-28742800	Enhancers	HSMMtube	muscle
19	chr22:28741000-28741800	Enhancers	Rectal Smooth Muscle	rectum
20	chr22:28741000-28742200	Weak transcription	Fetal Heart	heart
21	chr22:28741200-28742000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr22:28741200-28742800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr22:28741400-28741800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr22:28741400-28742800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr22:28741400-28744000	Weak transcription	Brain Hippocampus Middle	brain
26	chr22:28741600-28741800	Enhancers	NHDF-Ad	bronchial
27	chr22:28741600-28742200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr22:28741600-28742200	Weak transcription	Right Ventricle	heart
29	chr22:28741600-28742400	Weak transcription	Fetal Muscle Leg	muscle
30	chr22:28741600-28742400	Weak transcription	Psoas Muscle	Psoas
31	chr22:28741600-28743200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr22:28741600-28743800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr22:28741600-28744000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr22:28741600-28744800	Weak transcription	Ovary	ovary
35	chr22:28741600-28747600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr22:28741600-28752000	Weak transcription	HSMM	muscle
37	chr22:28741600-28753200	Weak transcription	Brain Germinal Matrix	brain
38	chr22:28741600-28759000	Weak transcription	Fetal Stomach	stomach

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