Variant report

Variant	rs5762478
Chromosome Location	chr22:28500281-28500282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1072967	0.90[CHB][hapmap]
rs11912165	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2064360	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2294820	0.81[AFR][1000 genomes]
rs2294969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28720063	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56695231	0.89[ASN][1000 genomes]
rs5752658	1.00[CEU][hapmap]
rs5752679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs5752687	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs5752690	0.89[ASN][1000 genomes]
rs5752693	0.98[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs5752710	0.82[YRI][hapmap]
rs5752718	1.00[JPT][hapmap]
rs5762408	1.00[CEU][hapmap]
rs5762446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs5762449	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs5762474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5762495	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5762498	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5762504	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762506	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5762508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5762532	0.85[YRI][hapmap]
rs5762540	0.91[CHB][hapmap]
rs59105820	0.86[AFR][1000 genomes]
rs9608667	1.00[YRI][hapmap]

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

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28466600-28503600	Weak transcription	Hela-S3	cervix
2	chr22:28472800-28501000	Weak transcription	Gastric	stomach
3	chr22:28485800-28501400	Strong transcription	Dnd41	blood
4	chr22:28485800-28508600	Weak transcription	Brain Substantia Nigra	brain
5	chr22:28486000-28507200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr22:28486200-28504400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:28486200-28504800	Weak transcription	Osteobl	bone
8	chr22:28486400-28508600	Weak transcription	Psoas Muscle	Psoas
9	chr22:28487400-28501200	Strong transcription	Fetal Muscle Trunk	muscle
10	chr22:28487600-28504400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr22:28487600-28517200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr22:28487800-28505000	Weak transcription	Colonic Mucosa	Colon
13	chr22:28488800-28501000	Weak transcription	Brain Hippocampus Middle	brain
14	chr22:28489000-28508200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr22:28489600-28500800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr22:28489800-28508400	Weak transcription	Small Intestine	intestine
17	chr22:28490600-28504400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr22:28491200-28503000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr22:28491600-28502000	Strong transcription	Fetal Intestine Large	intestine
20	chr22:28492600-28503200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr22:28492800-28501400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr22:28493600-28504200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr22:28493800-28502000	Strong transcription	Fetal Intestine Small	intestine
24	chr22:28494400-28503800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr22:28495000-28504000	Weak transcription	Fetal Brain Male	brain
26	chr22:28495000-28507600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr22:28495000-28508400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr22:28495000-28508400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr22:28495000-28508600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr22:28495200-28501000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr22:28495200-28501000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr22:28495200-28501200	Weak transcription	Right Ventricle	heart
33	chr22:28495200-28508600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr22:28495400-28500600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr22:28495600-28503000	Weak transcription	Liver	Liver
36	chr22:28496000-28500600	Weak transcription	Brain Angular Gyrus	brain
37	chr22:28496000-28500800	Weak transcription	Fetal Kidney	kidney
38	chr22:28496000-28501000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr22:28496000-28501000	Weak transcription	Pancreas	Pancrea
40	chr22:28496000-28505600	Weak transcription	Primary T cells from cord blood	blood
41	chr22:28496200-28501000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr22:28496600-28517200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr22:28496800-28500600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr22:28497200-28508600	Weak transcription	Stomach Mucosa	stomach
45	chr22:28497400-28504200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr22:28497600-28501000	Weak transcription	Lung	lung
47	chr22:28498000-28500800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr22:28498000-28503000	Weak transcription	Aorta	Aorta
49	chr22:28498200-28510800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr22:28498400-28500400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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