Variant report

Variant	rs134545
Chromosome Location	chr22:28799080-28799081
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs134196	0.81[CEU][hapmap]
rs134527	0.85[CEU][hapmap]
rs134529	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs134544	0.85[CEU][hapmap]
rs134551	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1807603	0.89[AFR][1000 genomes]
rs1986052	0.87[ASN][1000 genomes]
rs2145161	0.85[EUR][1000 genomes]
rs2180460	0.94[JPT][hapmap]
rs2346397	0.84[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs5752745	0.89[JPT][hapmap]
rs5752746	0.85[CEU][hapmap]
rs5752764	0.86[EUR][1000 genomes]
rs5762629	0.89[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs5762665	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5762680	0.86[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap]
rs5762730	0.86[EUR][1000 genomes]
rs5762741	0.80[EUR][1000 genomes]
rs6005754	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs6005795	0.94[ASN][1000 genomes]
rs695272	0.81[AMR][1000 genomes]
rs695388	0.85[CEU][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	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
rs134545	TTC28	cis	cerebellum	SCAN
rs134545	TTC28	cis	lymphoblastoid	seeQTL
rs134545	SEC14L4	cis	cerebellum	SCAN

Chromatin state (count:23 , 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	chr22:28799000-28799400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr22:28799000-28799400	Weak transcription	Psoas Muscle	Psoas

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