Variant report

Variant	rs5762540
Chromosome Location	chr22:28661884-28661885
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1072967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11912165	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2064360	0.90[CHB][hapmap]
rs2294969	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs28720063	0.84[ASN][1000 genomes]
rs5752718	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs5762474	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5762478	0.91[CHB][hapmap]
rs5762492	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs5762498	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs5762506	0.84[ASN][1000 genomes]
rs5762508	0.91[CHB][hapmap]
rs5762568	0.81[EUR][1000 genomes]
rs5762632	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs5997354	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60891699	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

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:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28618400-28662200	Weak transcription	Pancreas	Pancrea
2	chr22:28644400-28662400	Weak transcription	Psoas Muscle	Psoas
3	chr22:28646000-28664000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr22:28651600-28663000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr22:28651800-28690600	Weak transcription	Dnd41	blood
6	chr22:28653000-28664200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr22:28653000-28665000	Weak transcription	Fetal Muscle Leg	muscle
8	chr22:28653000-28671600	Weak transcription	Fetal Stomach	stomach
9	chr22:28656200-28662400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr22:28656800-28666000	Weak transcription	Small Intestine	intestine
11	chr22:28657000-28662400	Weak transcription	Adipose Nuclei	Adipose
12	chr22:28657000-28664200	Weak transcription	Brain Angular Gyrus	brain
13	chr22:28657000-28691600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr22:28657200-28662600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr22:28657200-28664000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr22:28659400-28671200	Weak transcription	Fetal Lung	lung
17	chr22:28660800-28662800	Weak transcription	Colon Smooth Muscle	Colon
18	chr22:28661400-28664000	Weak transcription	Aorta	Aorta
19	chr22:28661600-28662400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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