Variant report

Variant	rs1965072
Chromosome Location	chr3:54679831-54679832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10865990	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs11718583	0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs17054369	0.90[CHB][hapmap]
rs1820616	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs1882321	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1965073	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1997463	0.91[CHB][hapmap]
rs488451	0.90[ASN][1000 genomes]
rs492885	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4955890	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs510605	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs525736	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs529098	0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs530868	0.89[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.88[ASN][1000 genomes]
rs533524	0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs535526	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs541957	0.91[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs543828	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs550728	0.90[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs562668	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs566448	0.86[CHB][hapmap]
rs566884	0.91[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs568051	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs588784	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs593629	0.82[ASN][1000 genomes]
rs596992	0.88[ASN][1000 genomes]
rs599573	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs601383	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs601420	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs608142	0.91[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs622326	0.94[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs623696	0.91[ASN][1000 genomes]
rs630987	0.87[ASN][1000 genomes]
rs634393	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs646220	0.82[ASN][1000 genomes]
rs647480	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs652364	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs666071	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7633762	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs838017	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9882650	0.91[CHB][hapmap];0.86[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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1965072	C3orf51	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54663600-54683800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:54676800-54683200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:54677200-54685600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:54677400-54690800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:54677800-54681000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:54677800-54687800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:54678000-54680800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:54678400-54680200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
9	chr3:54678400-54683200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
10	chr3:54679200-54680600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
11	chr3:54679200-54685800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:54679600-54681000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:54679600-54685400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:54679800-54680600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:54679800-54681000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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