Variant report

Variant	rs5762416
Chromosome Location	chr22:28337711-28337712
allele	A/C
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:24)

rs_ID	r²[population]
rs1028364	0.80[ASN][1000 genomes]
rs118839	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs138631	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs138638	0.89[CEU][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs138650	0.94[ASW][hapmap];0.89[CEU][hapmap];0.83[CHD][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs138675	0.83[ASN][1000 genomes]
rs138685	0.81[ASW][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap]
rs1548235	0.83[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.80[ASN][1000 genomes]
rs2038158	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2267121	0.91[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs2267124	0.93[ASN][1000 genomes]
rs3747141	0.83[CHD][hapmap]
rs4140571	0.89[CEU][hapmap];0.88[CHD][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs470100	0.81[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs470105	0.81[CHD][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs5752667	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5762393	0.86[ASN][1000 genomes]
rs5762418	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5997319	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs6005671	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs720621	0.91[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73425788	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs738451	0.88[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs957601	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5762416	ZNF280A	cis	cerebellum	SCAN
rs5762416	MED30	trans	cerebellum	SCAN
rs5762416	TTC28AS	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28316400-28342600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr22:28316400-28358600	Weak transcription	Placenta	Placenta
3	chr22:28316400-28370200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr22:28316400-28376800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr22:28316400-28378000	Weak transcription	Esophagus	oesophagus
6	chr22:28316600-28348400	Weak transcription	Brain Substantia Nigra	brain
7	chr22:28316800-28340400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr22:28317000-28338800	Weak transcription	Fetal Intestine Small	intestine
9	chr22:28317000-28340800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr22:28317000-28348200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr22:28317600-28340800	Weak transcription	Thymus	Thymus
12	chr22:28317800-28342600	Weak transcription	Small Intestine	intestine
13	chr22:28317800-28345200	Weak transcription	HepG2	liver
14	chr22:28318800-28382000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr22:28319600-28340800	Weak transcription	Fetal Thymus	thymus
16	chr22:28319600-28358000	Weak transcription	Brain Germinal Matrix	brain
17	chr22:28319600-28383000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr22:28320800-28347800	Weak transcription	HUVEC	blood vessel
19	chr22:28321000-28354800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr22:28321200-28358400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr22:28321400-28340400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr22:28321400-28379000	Weak transcription	Primary B cells from cord blood	blood
23	chr22:28321600-28345000	Weak transcription	Fetal Lung	lung
24	chr22:28321800-28342800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr22:28322000-28365200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr22:28322000-28366200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr22:28322200-28339600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr22:28323800-28346000	Weak transcription	Dnd41	blood
29	chr22:28326800-28368600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr22:28327000-28339200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr22:28327000-28348000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr22:28327000-28348400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr22:28327200-28339200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr22:28327400-28347800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr22:28329400-28340800	Weak transcription	Pancreas	Pancrea
36	chr22:28329400-28347800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr22:28329400-28348200	Weak transcription	Adipose Nuclei	Adipose
38	chr22:28329400-28377800	Weak transcription	Primary T cells from cord blood	blood
39	chr22:28329800-28344000	Weak transcription	Liver	Liver
40	chr22:28332200-28345400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr22:28332600-28343000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr22:28333600-28343400	Weak transcription	Fetal Heart	heart
43	chr22:28335200-28338200	Weak transcription	Fetal Stomach	stomach

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