Variant report

Variant	rs1436900
Chromosome Location	chr1:217058479-217058480
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1370150	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2043670	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2576264	0.94[ASW][hapmap];0.92[CEU][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2576265	0.83[EUR][1000 genomes]
rs2576266	0.94[EUR][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	nsv873179	chr1:217056893-217112871	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Optic nerve measurement (cup area)	20395239	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1436900	SNORA16B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217055600-217062200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:217056800-217058800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:217057000-217058800	Enhancers	Fetal Intestine Small	intestine
4	chr1:217057000-217061200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:217057400-217058600	Enhancers	HMEC	breast
6	chr1:217057600-217058600	Enhancers	NHEK	skin
7	chr1:217057600-217058800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:217057600-217058800	Enhancers	Duodenum Mucosa	Duodenum
9	chr1:217057800-217058600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:217057800-217058600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:217058000-217058600	Enhancers	Fetal Kidney	kidney
12	chr1:217058000-217062200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:217058200-217058800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:217058200-217067600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:217058400-217061600	Weak transcription	Fetal Intestine Large	intestine
16	chr1:217058400-217061800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:217058400-217062000	Weak transcription	Stomach Mucosa	stomach
18	chr1:217058400-217065200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:217058400-217067800	Weak transcription	Small Intestine	intestine

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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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