Variant report

Variant	rs599573
Chromosome Location	chr3:54707446-54707447
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10865990	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs11130432	1.00[CEU][hapmap]
rs11718583	0.81[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs17054369	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs1820616	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1882321	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]
rs1965072	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1965073	0.92[ASN][1000 genomes]
rs1997463	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs488451	0.94[ASN][1000 genomes]
rs492885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4955890	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs510605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs513324	0.82[GIH][hapmap]
rs525736	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs529098	0.94[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs530868	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs533524	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs535526	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs541957	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs543828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs550728	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs562668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs566448	0.91[CHB][hapmap]
rs566884	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs568051	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs588784	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593629	0.86[ASN][1000 genomes]
rs596992	0.88[ASN][1000 genomes]
rs601383	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608142	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs622326	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs623696	0.89[ASN][1000 genomes]
rs630987	1.00[CEU][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs634393	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs646220	0.86[ASN][1000 genomes]
rs647480	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs652364	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs666071	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7633762	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs838017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9882650	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[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

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54704800-54710200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr3:54705000-54710400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:54705000-54719000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:54705600-54718800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:54705800-54710000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:54706000-54707800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:54706000-54708800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:54706000-54721600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:54706200-54707800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:54706200-54708200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:54706200-54718400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:54706200-54719400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:54706600-54713000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:54706800-54707800	Weak transcription	Right Atrium	heart
15	chr3:54706800-54708800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:54707200-54709600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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