Variant report

Variant	rs134488
Chromosome Location	chr22:28728344-28728345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10212083	0.91[CEU][hapmap]
rs10483148	1.00[CHB][hapmap]
rs10483150	1.00[CHB][hapmap]
rs10483151	0.83[CEU][hapmap]
rs12166475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs12167532	0.80[EUR][1000 genomes]
rs12167735	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs12168708	0.81[AMR][1000 genomes]
rs12170637	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1297607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134194	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs134197	0.83[CEU][hapmap];1.00[MEX][hapmap]
rs134501	1.00[CHB][hapmap]
rs134503	1.00[CHB][hapmap]
rs134504	1.00[CHB][hapmap]
rs134506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134509	1.00[CHB][hapmap]
rs134510	1.00[CHB][hapmap]
rs134514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134520	1.00[CHB][hapmap]
rs134521	1.00[CHB][hapmap]
rs134524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134528	1.00[CHB][hapmap]
rs134547	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs135641	1.00[CHB][hapmap]
rs135642	1.00[CHB][hapmap]
rs135644	1.00[CHB][hapmap]
rs135645	1.00[CHB][hapmap]
rs135649	1.00[CHB][hapmap]
rs1569700	1.00[CHB][hapmap]
rs16986077	1.00[MEX][hapmap]
rs16986177	1.00[CHB][hapmap]
rs16986254	1.00[CHB][hapmap]
rs16986257	1.00[CHB][hapmap]
rs16986266	1.00[CHB][hapmap]
rs16986308	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16986398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs17413461	0.83[CEU][hapmap]
rs17487463	0.83[CEU][hapmap]
rs2013784	1.00[CEU][hapmap]
rs2144922	1.00[CEU][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs7285440	1.00[CHB][hapmap]
rs7289625	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7291268	0.91[CEU][hapmap]
rs73430118	0.80[EUR][1000 genomes]
rs738200	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs79104	1.00[CHB][hapmap]
rs79107	1.00[CHB][hapmap]
rs9306457	0.91[CEU][hapmap]
rs9620778	0.91[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs9620779	0.91[CEU][hapmap]
rs9620797	0.91[CEU][hapmap]
rs9620804	0.91[CEU][hapmap]
rs9625433	0.83[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs9625437	0.91[CEU][hapmap]
rs9625438	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs9625440	0.83[CEU][hapmap]
rs9625447	0.83[CEU][hapmap]
rs9625467	0.91[CEU][hapmap]
rs9625475	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs9625477	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs9625478	0.83[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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs134488	TTC28	cis	lymphoblastoid	seeQTL
rs134488	C22orf15	cis	cerebellum	SCAN
rs134488	TMEM211	cis	cerebellum	SCAN
rs134488	SEZ6L	cis	cerebellum	SCAN
rs134488	TXNDC2	trans	cerebellum	SCAN
rs134488	GAL3ST1	cis	cerebellum	SCAN
rs134488	TFIP11	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28724800-28729600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr22:28725800-28728800	Weak transcription	Fetal Heart	heart
3	chr22:28726000-28728400	Weak transcription	Brain Anterior Caudate	brain
4	chr22:28726000-28728600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr22:28726000-28728600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr22:28726000-28728800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr22:28726200-28737400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr22:28726400-28728800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr22:28726400-28728800	Weak transcription	Brain Angular Gyrus	brain
10	chr22:28726400-28729400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr22:28726600-28728600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr22:28726600-28728600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr22:28726600-28728600	Weak transcription	Fetal Brain Female	brain
14	chr22:28727400-28729000	Enhancers	Brain Hippocampus Middle	brain
15	chr22:28727600-28729600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr22:28727800-28728600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr22:28727800-28729000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr22:28727800-28729000	Enhancers	Adipose Nuclei	Adipose
19	chr22:28727800-28729600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr22:28728000-28728400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr22:28728000-28728400	Weak transcription	Brain Substantia Nigra	brain
22	chr22:28728000-28728800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr22:28728200-28728600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr22:28728200-28729600	Enhancers	Fetal Lung	lung

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