Variant report

Variant	rs492885
Chromosome Location	chr3:54705906-54705907
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]
rs11718583	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17054369	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs1820616	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs1882321	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1965072	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1965073	0.90[ASN][1000 genomes]
rs1997463	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs488451	0.92[ASN][1000 genomes]
rs4955890	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs510605	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs525736	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs529098	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs530868	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs533524	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs535526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs541957	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs543828	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs550728	0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs562668	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs566448	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs566884	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs568051	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs588784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs593629	0.84[ASN][1000 genomes]
rs596992	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs599573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs601383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs601420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs608142	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs622326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs623696	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs630987	0.89[ASN][1000 genomes]
rs634393	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs646220	0.84[ASN][1000 genomes]
rs647480	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs652364	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs666071	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6784130	0.82[CEU][hapmap]
rs737517	0.85[CEU][hapmap]
rs7633762	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs838017	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs9882650	0.95[CHB][hapmap];0.91[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:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54702400-54706600	Enhancers	H9 Cell Line	embryonic stem cell
2	chr3:54702800-54706000	Enhancers	H1 Cell Line	embryonic stem cell
3	chr3:54703000-54706000	Enhancers	Fetal Stomach	stomach
4	chr3:54703200-54706000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:54703400-54706000	Enhancers	Fetal Lung	lung
6	chr3:54703800-54706200	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:54704000-54706200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:54704000-54706200	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr3:54704000-54706200	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr3:54704000-54706800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:54704200-54706200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:54704200-54706800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:54704200-54707200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:54704400-54706000	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr3:54704600-54706000	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr3:54704800-54710200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:54705000-54706400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:54705000-54710400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr3:54705000-54719000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:54705200-54706000	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr3:54705200-54706800	Enhancers	Right Atrium	heart
22	chr3:54705400-54706200	Enhancers	Hela-S3	cervix
23	chr3:54705600-54706000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:54705600-54706000	Enhancers	Esophagus	oesophagus
25	chr3:54705600-54718800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:54705800-54710000	Weak transcription	Rectal Mucosa Donor 29	rectum

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