Variant report

Variant	rs6662665
Chromosome Location	chr1:76068279-76068280
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:76066835..76069254-chr1:76079406..76081859,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10493575	1.00[JPT][hapmap]
rs11578532	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12401888	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12401896	1.00[JPT][hapmap]
rs12406883	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12406884	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408190	1.00[JPT][hapmap]
rs12410333	1.00[JPT][hapmap]
rs1443845	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs1576927	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17303788	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs17584320	1.00[JPT][hapmap]
rs17644957	1.00[JPT][hapmap]
rs184159	1.00[JPT][hapmap]
rs1857353	1.00[JPT][hapmap]
rs1857354	1.00[JPT][hapmap]
rs190024	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1913118	1.00[JPT][hapmap]
rs1930323	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1936359	1.00[JPT][hapmap]
rs2024773	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2040079	1.00[JPT][hapmap]
rs2040082	1.00[JPT][hapmap]
rs211688	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs211702	1.00[JPT][hapmap]
rs211744	1.00[JPT][hapmap]
rs211752	1.00[JPT][hapmap]
rs211771	1.00[JPT][hapmap]
rs2779490	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35425390	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs388916	0.90[AMR][1000 genomes]
rs407954	0.90[AMR][1000 genomes]
rs449119	0.90[AMR][1000 genomes]
rs449394	1.00[JPT][hapmap];0.93[YRI][hapmap]
rs4540592	1.00[JPT][hapmap]
rs4949855	1.00[JPT][hapmap]
rs55694101	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6593581	0.90[AMR][1000 genomes]
rs6593583	0.85[AMR][1000 genomes]
rs6682395	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687877	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74091759	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74091760	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74091761	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74091769	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs983331	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv3445096	chr1:75933216-76126980	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2757737	chr1:75986904-76187748	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758943	chr1:75986904-76187748	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6662665	IFI44	cis	parietal	SCAN
rs6662665	CRYZ	cis	lymphoblastoid	seeQTL
rs6662665	SLC44A5	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links