Variant report

Variant	rs134541
Chromosome Location	chr22:28795263-28795264
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1125250	0.95[CEU][hapmap];0.89[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1303845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs134179	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs134180	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs134183	0.95[CEU][hapmap]
rs134196	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs134489	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs134500	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs134507	1.00[CEU][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs134526	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs134543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs134548	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs134551	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17503350	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2346397	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2346867	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34593692	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5752743	0.85[JPT][hapmap]
rs5762629	0.83[CEU][hapmap]
rs5762660	0.85[JPT][hapmap]
rs5762680	0.83[CEU][hapmap]
rs695272	0.97[ASN][1000 genomes]
rs695439	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs695591	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs695625	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs695659	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs695762	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs695796	0.94[ASN][1000 genomes]
rs695797	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs134541	TTC28	cis	lymphoblastoid	seeQTL
rs134541	TTC28	cis	cerebellum	SCAN
rs134541	SEC14L4	cis	parietal	SCAN
rs134541	TTC7B	trans	parietal	SCAN

Chromatin state (count:34 , 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	chr22:28792000-28795400	Enhancers	Brain Hippocampus Middle	brain
8	chr22:28792000-28795600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr22:28792400-28795400	Enhancers	Fetal Brain Male	brain
10	chr22:28792600-28801800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:28792800-28795400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr22:28792800-28795400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr22:28792800-28805200	Weak transcription	Fetal Intestine Large	intestine
14	chr22:28793000-28798000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr22:28793000-28808200	Weak transcription	Aorta	Aorta
16	chr22:28793000-28808600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr22:28793000-28814000	Weak transcription	Left Ventricle	heart
18	chr22:28793000-28819800	Weak transcription	Fetal Intestine Small	intestine
19	chr22:28793400-28797400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr22:28793400-28806200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr22:28794200-28806000	Weak transcription	NHDF-Ad	bronchial
22	chr22:28794600-28795400	Weak transcription	Gastric	stomach
23	chr22:28794600-28795600	Enhancers	Liver	Liver
24	chr22:28794600-28797600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr22:28794600-28804600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr22:28794600-28804800	Weak transcription	Fetal Stomach	stomach
27	chr22:28794600-28806000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr22:28794600-28806000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr22:28795000-28796000	Weak transcription	Fetal Brain Female	brain
30	chr22:28795000-28803400	Weak transcription	Brain Anterior Caudate	brain
31	chr22:28795200-28795400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr22:28795200-28795400	Enhancers	Brain Angular Gyrus	brain
33	chr22:28795200-28798000	Weak transcription	Dnd41	blood
34	chr22:28795200-28803200	Weak transcription	Brain Inferior Temporal Lobe	brain

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