Variant report

Variant	rs1980549
Chromosome Location	chr1:55945134-55945135
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1165390	0.89[EUR][1000 genomes]
rs1165391	0.89[EUR][1000 genomes]
rs1695937	0.90[EUR][1000 genomes]
rs1695939	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1695958	0.82[ASN][1000 genomes]
rs1695960	0.82[ASN][1000 genomes]
rs1740118	0.82[ASN][1000 genomes]
rs1740123	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1740126	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1780520	0.91[EUR][1000 genomes]
rs1780524	0.90[EUR][1000 genomes]
rs1780526	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1780534	0.87[ASN][1000 genomes]
rs2649629	0.86[CHB][hapmap];0.85[GIH][hapmap]
rs2748703	0.82[ASN][1000 genomes]
rs2800838	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800840	0.82[ASN][1000 genomes]
rs4325177	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1008241	chr1:55922008-55972596	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1980549	DHCR24	cis	frontal cortex	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:55940000-55950000	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:55940400-55946600	Weak transcription	Osteobl	bone
3	chr1:55941000-55946800	Enhancers	Fetal Intestine Large	intestine
4	chr1:55942000-55946800	Enhancers	Fetal Intestine Small	intestine
5	chr1:55942200-55946000	Weak transcription	Pancreas	Pancrea
6	chr1:55942400-55946000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:55943200-55945800	Weak transcription	Fetal Lung	lung
8	chr1:55943600-55946400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:55944000-55946800	Enhancers	HepG2	liver
10	chr1:55944200-55945800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:55944200-55950600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:55944600-55945600	Weak transcription	NHDF-Ad	bronchial
13	chr1:55944800-55945200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:55944800-55946000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:55944800-55947000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr1:55945000-55945800	Weak transcription	Fetal Kidney	kidney
17	chr1:55945000-55946400	Weak transcription	HSMM	muscle
18	chr1:55945000-55946800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:55945000-55950200	Weak transcription	H1 BMP4 Derived Trophoblast 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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