Variant report

Variant	rs3014267
Chromosome Location	chr1:227552917-227552918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10495255	0.83[JPT][hapmap]
rs12035986	0.93[JPT][hapmap]
rs12044287	0.83[JPT][hapmap]
rs12137591	0.83[JPT][hapmap]
rs12565871	0.82[JPT][hapmap]
rs2953638	0.89[JPT][hapmap]
rs2953643	0.80[ASN][1000 genomes]
rs2953645	0.80[ASN][1000 genomes]
rs2953650	0.83[ASN][1000 genomes]
rs2953652	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2953655	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2953656	0.86[ASN][1000 genomes]
rs3014252	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs3014253	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs3014256	0.89[JPT][hapmap]
rs3014263	0.80[ASN][1000 genomes]
rs3795457	0.80[JPT][hapmap]
rs4339829	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3014267	C1orf65	cis	cerebellum	SCAN
rs3014267	HHIPL2	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227545800-227571200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:227552400-227553800	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr1:227552600-227553000	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr1:227552600-227553200	Enhancers	Colonic Mucosa	Colon
5	chr1:227552600-227553800	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr1:227552600-227556400	Weak transcription	K562	blood

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