Variant report

Variant	rs11207925
Chromosome Location	chr1:62669243-62669244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10889298	0.85[AMR][1000 genomes]
rs10889299	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10889300	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207924	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11207926	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11207930	0.82[ASN][1000 genomes]
rs11207931	0.83[ASN][1000 genomes]
rs11207932	0.83[ASN][1000 genomes]
rs11207936	0.83[ASN][1000 genomes]
rs11802658	0.83[ASN][1000 genomes]
rs11803019	0.83[ASN][1000 genomes]
rs11805853	0.83[ASN][1000 genomes]
rs11806202	0.83[ASN][1000 genomes]
rs11809029	0.83[ASN][1000 genomes]
rs17123184	0.81[ASN][1000 genomes]
rs56011715	0.83[ASN][1000 genomes]
rs59949671	0.83[ASN][1000 genomes]
rs74079019	0.83[ASN][1000 genomes]
rs7516863	0.83[ASN][1000 genomes]
rs7539677	0.82[ASN][1000 genomes]
rs7551777	0.83[ASN][1000 genomes]

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	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	nsv870842	chr1:62644118-62679202	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11207925	L1TD1	cis	Thyroid	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62661000-62675600	Weak transcription	Right Atrium	heart
2	chr1:62664000-62673000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:62664600-62669800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:62664800-62677800	Weak transcription	Placenta	Placenta
5	chr1:62665200-62672400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:62665400-62669600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:62665800-62670400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:62666000-62695400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:62666800-62672000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:62667000-62672400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:62667000-62674200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:62667400-62676200	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr1:62667600-62669600	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr1:62667600-62672800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:62668200-62670200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:62668200-62672200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:62668400-62669800	Strong transcription	Fetal Stomach	stomach
18	chr1:62668400-62670400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:62668400-62671400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:62668400-62677200	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr1:62668600-62670600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:62668800-62669600	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:62668800-62670200	Strong transcription	Fetal Lung	lung
24	chr1:62668800-62670600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:62669000-62670200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:62669000-62670400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:62669000-62674600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:62669000-62675600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:62669200-62669400	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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