Variant report

Variant	rs5762511
Chromosome Location	chr22:28575543-28575544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs135654	1.00[YRI][hapmap]
rs16986354	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs2294818	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5762511	TTC28AS	cis	cerebellum	SCAN
rs5762511	HPS4	cis	parietal	SCAN
rs5762511	AP1B1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28559800-28577400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr22:28567000-28577600	Weak transcription	Psoas Muscle	Psoas
3	chr22:28568200-28579000	Weak transcription	Left Ventricle	heart
4	chr22:28569000-28577600	Weak transcription	Small Intestine	intestine
5	chr22:28569400-28577600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr22:28569400-28577600	Weak transcription	Ovary	ovary
7	chr22:28569400-28579200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr22:28569600-28577200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr22:28569600-28577200	Weak transcription	Fetal Lung	lung
10	chr22:28570000-28577400	Weak transcription	Adipose Nuclei	Adipose
11	chr22:28570000-28581000	Weak transcription	Fetal Intestine Small	intestine
12	chr22:28572200-28597800	Weak transcription	Dnd41	blood
13	chr22:28572400-28577600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr22:28572600-28575600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr22:28575200-28575600	Enhancers	Pancreas	Pancrea
16	chr22:28575400-28575600	Enhancers	Thymus	Thymus
17	chr22:28575400-28575800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

Quick Search:

Input of quick search could be:

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

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