Variant report

Variant	rs12753484
Chromosome Location	chr1:62689811-62689812
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-L1TD1-3	chr1:62689706-62690135	NONHSAT003631

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10889302	0.97[ASN][1000 genomes]
rs10889303	0.97[ASN][1000 genomes]
rs10889305	0.97[ASN][1000 genomes]
rs10889309	0.82[AMR][1000 genomes]
rs11207938	0.91[ASN][1000 genomes]
rs11207940	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12040080	1.00[ASN][1000 genomes]
rs12041005	0.90[ASN][1000 genomes]
rs12043306	0.95[ASN][1000 genomes]
rs12048000	1.00[ASN][1000 genomes]
rs12089897	0.81[AMR][1000 genomes]
rs12133752	1.00[ASN][1000 genomes]
rs12144690	1.00[ASN][1000 genomes]
rs2067994	0.81[AMR][1000 genomes]
rs2365990	1.00[ASN][1000 genomes]
rs2774928	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28562952	1.00[ASN][1000 genomes]
rs4019803	1.00[ASN][1000 genomes]
rs4915803	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4915806	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55675042	0.98[ASN][1000 genomes]
rs55831250	0.98[ASN][1000 genomes]
rs6669211	0.94[ASN][1000 genomes]
rs72679772	0.97[ASN][1000 genomes]
rs72679773	0.93[ASN][1000 genomes]
rs72679787	1.00[ASN][1000 genomes]
rs72679795	1.00[ASN][1000 genomes]
rs72679796	1.00[ASN][1000 genomes]
rs7411110	1.00[ASN][1000 genomes]
rs7516473	0.95[ASN][1000 genomes]
rs7528199	0.95[ASN][1000 genomes]
rs7538818	0.95[ASN][1000 genomes]
rs7539028	1.00[ASN][1000 genomes]
rs7541340	1.00[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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62666000-62695400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:62677200-62693400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:62677200-62694000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:62677200-62694000	Weak transcription	Fetal Lung	lung
5	chr1:62682400-62694600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:62683200-62693600	Weak transcription	Fetal Stomach	stomach
7	chr1:62684200-62691600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:62685000-62692000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:62689200-62690000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:62689200-62693600	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr1:62689200-62693800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:62689200-62694000	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:62689400-62694200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:62689400-62694400	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr1:62689400-62695800	Weak transcription	Colonic Mucosa	Colon
16	chr1:62689600-62690200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr1:62689600-62691000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:62689600-62691200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:62689600-62694000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:62689600-62694400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:62689600-62695600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:62689800-62690000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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