Variant report

Variant	rs528264
Chromosome Location	chr2:30928787-30928788
allele	C/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:15)

rs_ID	r²[population]
rs1252298	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs485243	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs497707	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs514940	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs528514	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs537833	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs540977	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs543134	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs544395	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs546467	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs547360	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs566241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs566934	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs578011	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs935984	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs528264	LCLAT1	cis	parietal	SCAN
rs528264	CCDC121	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30902400-30954000	Weak transcription	Gastric	stomach
2	chr2:30926600-30935800	Weak transcription	Primary B cells from cord blood	blood
3	chr2:30926800-30934800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr2:30927200-30930800	Enhancers	Fetal Heart	heart
5	chr2:30927600-30929000	Enhancers	Fetal Muscle Leg	muscle
6	chr2:30928000-30928800	Enhancers	Right Ventricle	heart
7	chr2:30928000-30929600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:30928000-30930000	Enhancers	Left Ventricle	heart
9	chr2:30928000-30931400	Weak transcription	NHLF	lung
10	chr2:30928200-30928800	Enhancers	Right Atrium	heart
11	chr2:30928200-30929000	Enhancers	Stomach Smooth Muscle	stomach
12	chr2:30928200-30929200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:30928200-30929200	Weak transcription	NHDF-Ad	bronchial
14	chr2:30928200-30929600	Weak transcription	Placenta	Placenta
15	chr2:30928200-30929600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:30928400-30929200	Weak transcription	Aorta	Aorta
17	chr2:30928400-30929600	Weak transcription	Ovary	ovary
18	chr2:30928600-30930600	Enhancers	Fetal Muscle Trunk	muscle

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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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