Variant report

Variant	rs646220
Chromosome Location	chr3:54731908-54731909
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11718583	0.85[ASN][1000 genomes]
rs1965072	0.82[ASN][1000 genomes]
rs1965073	0.81[ASN][1000 genomes]
rs488451	0.89[ASN][1000 genomes]
rs492885	0.84[ASN][1000 genomes]
rs510605	0.86[ASN][1000 genomes]
rs525736	0.97[ASN][1000 genomes]
rs530868	0.81[ASN][1000 genomes]
rs533524	0.82[ASN][1000 genomes]
rs543828	0.83[ASN][1000 genomes]
rs550728	0.96[ASN][1000 genomes]
rs562668	0.84[ASN][1000 genomes]
rs566884	0.92[ASN][1000 genomes]
rs568051	0.97[ASN][1000 genomes]
rs588784	0.86[ASN][1000 genomes]
rs593629	0.97[ASN][1000 genomes]
rs599573	0.86[ASN][1000 genomes]
rs601383	0.86[ASN][1000 genomes]
rs601420	0.86[ASN][1000 genomes]
rs608142	0.94[ASN][1000 genomes]
rs622326	0.80[ASN][1000 genomes]
rs630987	0.81[ASN][1000 genomes]
rs634393	0.90[ASN][1000 genomes]
rs652364	0.94[ASN][1000 genomes]
rs666071	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs838017	0.82[ASN][1000 genomes]

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:25 , 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	chr3:54730000-54734000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:54730200-54732400	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr3:54730400-54732000	Enhancers	H9 Cell Line	embryonic stem cell
5	chr3:54730400-54732800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:54731000-54732000	Weak transcription	HepG2	liver
7	chr3:54731200-54733200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:54731400-54732400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr3:54731400-54733600	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:54731400-54733600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:54731600-54732000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:54731600-54732000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr3:54731600-54732200	Enhancers	Brain Anterior Caudate	brain
14	chr3:54731600-54732400	Enhancers	Brain Germinal Matrix	brain
15	chr3:54731600-54732600	Enhancers	Fetal Brain Male	brain
16	chr3:54731600-54732800	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:54731600-54732800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr3:54731600-54733400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:54731600-54733600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr3:54731600-54733600	Enhancers	Fetal Brain Female	brain
21	chr3:54731800-54732000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:54731800-54733000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:54731800-54733200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:54731800-54733200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:54731800-54733200	Enhancers	Cortex derived primary cultured neurospheres	brain

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