Variant report

Variant	rs550728
Chromosome Location	chr3:54730572-54730573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10865990	0.95[CHB][hapmap]
rs11130432	1.00[CEU][hapmap]
rs11718583	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17054369	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs1820616	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs1882321	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs1965072	0.90[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1965073	0.82[ASN][1000 genomes]
rs1997463	1.00[CHB][hapmap]
rs488451	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs492885	0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4955890	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs510605	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs525736	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529098	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs530868	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs533524	0.85[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs535526	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs541957	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs543828	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs562668	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs566448	0.85[CHB][hapmap]
rs566884	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs568051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs588784	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs593629	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs599573	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs601383	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs601420	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs608142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs622326	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs623696	0.80[ASN][1000 genomes]
rs630987	0.83[ASN][1000 genomes]
rs634393	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs646220	0.96[ASN][1000 genomes]
rs647480	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap]
rs652364	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs666071	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7633762	0.82[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs838017	0.82[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9836012	0.86[AMR][1000 genomes]
rs9882650	0.82[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54713600-54743400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:54725600-54731200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:54725800-54731600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:54725800-54731600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:54726000-54731400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:54726600-54731400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:54726800-54731400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:54728400-54731800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:54728800-54731600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:54729400-54731200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:54729800-54731800	Enhancers	HMEC	breast
12	chr3:54730000-54730800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:54730000-54731600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:54730000-54734000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:54730200-54730800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr3:54730200-54731000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:54730200-54732400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr3:54730400-54732000	Enhancers	H9 Cell Line	embryonic stem cell
19	chr3:54730400-54732800	Enhancers	HUES48 Cell Line	embryonic stem cell

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