Variant report

Variant	rs5762532
Chromosome Location	chr22:28628209-28628210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2294969	0.82[YRI][hapmap]
rs5752710	1.00[ASW][hapmap]
rs5752729	0.96[CEU][hapmap]
rs5762478	0.85[YRI][hapmap]
rs5762508	0.85[YRI][hapmap]
rs5762541	0.87[ASW][hapmap];0.87[YRI][hapmap]
rs6005754	0.95[JPT][hapmap]
rs715527	0.84[EUR][1000 genomes]
rs7288416	0.96[CEU][hapmap]
rs738199	0.81[CEU][hapmap]
rs738995	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs9306454	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs9608667	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9613570	0.92[CEU][hapmap]
rs9613574	0.81[CHB][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
rs5762532	TTC28	cis	cerebellum	SCAN
rs5762532	TFIP11	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28612200-28634800	Weak transcription	Dnd41	blood
2	chr22:28618400-28639600	Weak transcription	Ovary	ovary
3	chr22:28618400-28662200	Weak transcription	Pancreas	Pancrea
4	chr22:28619400-28631000	Weak transcription	Brain Hippocampus Middle	brain
5	chr22:28620400-28639200	Weak transcription	Left Ventricle	heart
6	chr22:28625400-28628400	Enhancers	Adipose Nuclei	Adipose
7	chr22:28625400-28628600	Enhancers	HSMM	muscle
8	chr22:28625400-28628600	Enhancers	NHLF	lung
9	chr22:28625600-28628600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr22:28625600-28628800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:28625800-28630800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr22:28626200-28628600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr22:28626200-28628800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr22:28626400-28628600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr22:28626400-28628800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr22:28626400-28632000	Weak transcription	Aorta	Aorta
17	chr22:28626600-28628600	Enhancers	NHDF-Ad	bronchial
18	chr22:28626600-28628600	Enhancers	Osteobl	bone
19	chr22:28627000-28628400	Enhancers	HepG2	liver
20	chr22:28627000-28628800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr22:28627200-28628600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr22:28627200-28628600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr22:28627200-28628600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr22:28627400-28628800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr22:28627600-28628600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr22:28627600-28628600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr22:28627600-28628600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr22:28627600-28628600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr22:28627600-28630600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr22:28627800-28628600	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr22:28627800-28628600	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr22:28628000-28628600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr22:28628000-28628600	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr22:28628000-28628600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr22:28628000-28639400	Weak transcription	Fetal Heart	heart
36	chr22:28628200-28628600	Enhancers	HSMMtube	muscle
37	chr22:28628200-28643200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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