Variant report

Variant	rs17188009
Chromosome Location	chr1:209378153-209378154
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:19)

rs_ID	r²[population]
rs10494918	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17188002	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17188016	0.82[EUR][1000 genomes]
rs17260224	0.87[CEU][hapmap];1.00[CHD][hapmap]
rs1933613	0.82[EUR][1000 genomes]
rs2800930	0.87[CEU][hapmap]
rs55933101	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56805778	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57720299	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59563227	0.89[EUR][1000 genomes]
rs59658508	1.00[ASN][1000 genomes]
rs6657861	0.87[EUR][1000 genomes]
rs6671102	0.94[ASN][1000 genomes]
rs73083997	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73085905	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73085915	0.81[AFR][1000 genomes]
rs73085916	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74155423	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74155426	0.85[EUR][1000 genomes];0.97[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	nsv832481	chr1:209371276-209540333	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17188009	SNORD116-29	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209370400-209380800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209373200-209380800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:209373200-209381200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:209373600-209380400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:209376200-209378200	Enhancers	Fetal Brain Female	brain
6	chr1:209376200-209378800	Enhancers	Fetal Brain Male	brain
7	chr1:209376800-209380400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:209377000-209380600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:209377000-209380800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:209377200-209381200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:209377400-209380800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:209377600-209380600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:209377800-209378400	Weak transcription	Fetal Stomach	stomach
14	chr1:209377800-209380400	Weak transcription	Brain Germinal Matrix	brain
15	chr1:209378000-209379000	Enhancers	Fetal Lung	lung

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