Variant report

Variant	rs5762498
Chromosome Location	chr22:28547410-28547411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1072967	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs11912165	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2064360	1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28720063	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56695231	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs5752679	1.00[CHB][hapmap]
rs5752687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs5752690	0.82[ASN][1000 genomes]
rs5752693	0.92[EUR][1000 genomes]
rs5762446	1.00[CHB][hapmap]
rs5762449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs5762474	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5762478	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5762492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5762495	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762504	0.90[ASN][1000 genomes]
rs5762506	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5762508	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs5762540	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs9613574	1.00[YRI][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

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28533800-28559000	Weak transcription	Aorta	Aorta
2	chr22:28536200-28549600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr22:28537200-28558800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr22:28538800-28549800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr22:28539200-28558400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr22:28539600-28549800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr22:28540200-28558600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr22:28540200-28567800	Weak transcription	Gastric	stomach
9	chr22:28540400-28550000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr22:28540800-28549800	Weak transcription	Psoas Muscle	Psoas
11	chr22:28540800-28567800	Weak transcription	Small Intestine	intestine
12	chr22:28541000-28553000	Weak transcription	Fetal Muscle Leg	muscle
13	chr22:28541000-28557200	Weak transcription	Lung	lung
14	chr22:28542800-28548000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr22:28543000-28549600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr22:28543200-28548200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr22:28543200-28548200	Weak transcription	Right Ventricle	heart
18	chr22:28543400-28548200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr22:28543400-28548200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr22:28543400-28550800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr22:28543400-28557600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr22:28543400-28559200	Weak transcription	Fetal Kidney	kidney
23	chr22:28543400-28568800	Weak transcription	NHDF-Ad	bronchial
24	chr22:28543600-28551000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr22:28543600-28559000	Weak transcription	Pancreas	Pancrea
26	chr22:28543800-28550800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr22:28543800-28551200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr22:28543800-28553600	Weak transcription	Brain Hippocampus Middle	brain
29	chr22:28543800-28558600	Weak transcription	Fetal Stomach	stomach
30	chr22:28543800-28567200	Weak transcription	Fetal Heart	heart
31	chr22:28544000-28552000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr22:28544200-28553200	Weak transcription	Brain Anterior Caudate	brain
33	chr22:28544400-28549800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr22:28545600-28548400	Enhancers	Fetal Brain Male	brain
35	chr22:28545800-28547800	Enhancers	Fetal Brain Female	brain
36	chr22:28546200-28547800	Enhancers	Rectal Smooth Muscle	rectum
37	chr22:28546400-28548400	Enhancers	Colon Smooth Muscle	Colon
38	chr22:28546600-28547600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr22:28546600-28547600	Enhancers	Adipose Nuclei	Adipose
40	chr22:28546600-28547800	Enhancers	Brain Germinal Matrix	brain
41	chr22:28546800-28547600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr22:28546800-28547600	Enhancers	HepG2	liver
43	chr22:28546800-28547800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr22:28546800-28553400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr22:28547000-28558600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr22:28547000-28558600	Weak transcription	Left Ventricle	heart
47	chr22:28547200-28547600	Weak transcription	Fetal Lung	lung
48	chr22:28547400-28547600	Enhancers	NHLF	lung
49	chr22:28547400-28551600	Weak transcription	Dnd41	blood
50	chr22:28547400-28552000	Weak transcription	Ovary	ovary

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