Variant report

Variant	rs2346395
Chromosome Location	chr22:28795080-28795081
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11703980	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17412920	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs17502181	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1997958	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2056962	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap]
rs2223369	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs5762541	0.85[CEU][hapmap]
rs5762656	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs5762686	1.00[ASW][hapmap];0.92[MEX][hapmap]
rs7288416	1.00[ASW][hapmap];0.85[MEX][hapmap]
rs73170603	0.87[AFR][1000 genomes]
rs738996	1.00[ASW][hapmap];0.83[MEX][hapmap]
rs9306454	1.00[ASW][hapmap];0.85[MEX][hapmap]
rs9608677	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]
rs9613574	1.00[CEU][hapmap]
rs9613580	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs9613588	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs9613617	1.00[MEX][hapmap]
rs9613630	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs9613640	1.00[AFR][1000 genomes];0.86[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2346395	TTC28	cis	cerebellum	SCAN
rs2346395	ZNF251	trans	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28789800-28796200	Enhancers	Fetal Lung	lung
2	chr22:28790400-28795400	Enhancers	Brain Substantia Nigra	brain
3	chr22:28790600-28795600	Enhancers	Ovary	ovary
4	chr22:28791400-28800400	Weak transcription	Fetal Muscle Leg	muscle
5	chr22:28791600-28795400	Weak transcription	Lung	lung
6	chr22:28791600-28797600	Weak transcription	Placenta	Placenta
7	chr22:28791800-28795200	Enhancers	Adipose Nuclei	Adipose
8	chr22:28791800-28795200	Enhancers	Dnd41	blood
9	chr22:28792000-28795200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr22:28792000-28795400	Enhancers	Brain Hippocampus Middle	brain
11	chr22:28792000-28795600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr22:28792200-28795200	Enhancers	Brain Cingulate Gyrus	brain
13	chr22:28792400-28795400	Enhancers	Fetal Brain Male	brain
14	chr22:28792600-28801800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr22:28792800-28795400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr22:28792800-28795400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr22:28792800-28805200	Weak transcription	Fetal Intestine Large	intestine
18	chr22:28793000-28798000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr22:28793000-28808200	Weak transcription	Aorta	Aorta
20	chr22:28793000-28808600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr22:28793000-28814000	Weak transcription	Left Ventricle	heart
22	chr22:28793000-28819800	Weak transcription	Fetal Intestine Small	intestine
23	chr22:28793400-28797400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr22:28793400-28806200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr22:28794200-28806000	Weak transcription	NHDF-Ad	bronchial
26	chr22:28794600-28795400	Weak transcription	Gastric	stomach
27	chr22:28794600-28795600	Enhancers	Liver	Liver
28	chr22:28794600-28797600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr22:28794600-28804600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr22:28794600-28804800	Weak transcription	Fetal Stomach	stomach
31	chr22:28794600-28806000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr22:28794600-28806000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr22:28794800-28795200	Weak transcription	Brain Angular Gyrus	brain
34	chr22:28795000-28795200	Enhancers	NHLF	lung
35	chr22:28795000-28795200	Enhancers	Osteobl	bone
36	chr22:28795000-28796000	Weak transcription	Fetal Brain Female	brain
37	chr22:28795000-28803400	Weak transcription	Brain Anterior Caudate	brain

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