Variant report

Variant	rs5762520
Chromosome Location	chr22:28603212-28603213
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs134522	0.92[CEU][hapmap]
rs135648	0.86[LWK][hapmap]
rs5762528	0.94[ASW][hapmap]
rs6005754	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv962867	chr22:28595811-28611386	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases
5	esv2314214	chr22:28603211-28603212	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5762520	TTC28	cis	lymphoblastoid	seeQTL
rs5762520	GGT5	cis	parietal	SCAN
rs5762520	TTC28	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28577000-28603600	Weak transcription	Aorta	Aorta
2	chr22:28600200-28616400	Weak transcription	Ovary	ovary
3	chr22:28602400-28603400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr22:28602400-28604400	Enhancers	HUVEC	blood vessel
5	chr22:28602600-28604600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr22:28602800-28604000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr22:28602800-28604600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr22:28603000-28603400	Weak transcription	NHDF-Ad	bronchial
9	chr22:28603000-28604000	Enhancers	Colon Smooth Muscle	Colon
10	chr22:28603000-28604400	Enhancers	NHLF	lung
11	chr22:28603000-28604600	Enhancers	NH-A	brain
12	chr22:28603000-28605400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr22:28603200-28603600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr22:28603200-28604600	Enhancers	Osteobl	bone
15	chr22:28603200-28605200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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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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