Variant report

Variant	rs28385324
Chromosome Location	chr5:58436136-58436137
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13176291	0.82[CEU][hapmap];0.90[MEX][hapmap]
rs13176475	0.82[CEU][hapmap];0.90[MEX][hapmap]
rs13361218	0.82[CEU][hapmap];0.95[MEX][hapmap]
rs1559251	0.82[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap]
rs1824788	0.83[CHD][hapmap]
rs1971940	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[ASN][1000 genomes]
rs4699935	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4700322	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6450506	0.82[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[MEX][hapmap]
rs716908	0.82[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap]
rs7707065	0.87[ASN][1000 genomes]
rs7728050	0.91[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs7730750	0.87[ASN][1000 genomes]
rs922434	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv881702	chr5:58432413-58474854	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28385324	LRRC70	cis	cerebellum	SCAN
rs28385324	CCNO	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58424000-58439800	Weak transcription	Small Intestine	intestine
2	chr5:58424000-58447000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58424200-58446200	Weak transcription	Fetal Intestine Large	intestine
4	chr5:58424200-58446600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:58427200-58454000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr5:58429800-58447200	Weak transcription	Left Ventricle	heart
7	chr5:58430000-58437000	Weak transcription	Colon Smooth Muscle	Colon
8	chr5:58430000-58442600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:58431000-58440000	Weak transcription	Fetal Lung	lung
10	chr5:58431200-58437400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:58433000-58451600	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:58434800-58437800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr5:58435000-58439600	Genic enhancers	A549	lung
14	chr5:58435200-58438000	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr5:58435200-58439000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:58435400-58437200	Weak transcription	Psoas Muscle	Psoas
17	chr5:58435400-58442400	Weak transcription	Hela-S3	cervix
18	chr5:58435800-58437600	Enhancers	Fetal Heart	heart
19	chr5:58436000-58439200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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

what's new

Quick links