Variant report

Variant	rs1146313
Chromosome Location	chr1:119026090-119026091
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10923578	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10923589	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1146308	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1146311	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1146315	0.86[ASW][hapmap];0.96[CEU][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11590559	0.80[EUR][1000 genomes]
rs11590971	0.81[EUR][1000 genomes]
rs1951938	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4659103	0.81[EUR][1000 genomes]
rs60820425	0.82[EUR][1000 genomes]
rs6660988	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6684700	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3494191	chr1:118772550-119719548	Enhancers Strong transcription Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv3494192	chr1:118772550-119719548	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1006143	chr1:118886864-119037964	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv535073	chr1:118886864-119037964	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1001757	chr1:118973624-119048181	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1004804	chr1:118975209-119048663	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1003425	chr1:118983592-119045934	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv535074	chr1:118983592-119045934	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1013186	chr1:119005483-119048663	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1146313	CASQ2	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:119025600-119026600	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr1:119025600-119026800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr1:119025800-119026200	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr1:119025800-119026600	Enhancers	H9 Cell Line	embryonic stem cell
5	chr1:119025800-119026600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:119025800-119026600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:119025800-119026800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:119026000-119026200	Enhancers	HMEC	breast
9	chr1:119026000-119026600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:119026000-119026600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:119026000-119026600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr1:119026000-119026600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:119026000-119026600	Enhancers	Placenta	Placenta
14	chr1:119026000-119026600	Enhancers	NHEK	skin
15	chr1:119026000-119026800	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:119026000-119026800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:119026000-119027000	Enhancers	HUES64 Cell Line	embryonic stem cell

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