Variant report

Variant	rs12137088
Chromosome Location	chr1:62666518-62666519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12737213	0.93[EUR][1000 genomes]
rs2457822	0.90[EUR][1000 genomes]
rs2481697	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2481707	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2481708	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2941681	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2989009	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6587958	0.82[EUR][1000 genomes]
rs6656763	0.89[CEU][hapmap];0.85[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12137088	L1TD1	Cis_1M	lymphoblastoid	RTeQTL
rs12137088	L1TD1	cis	multi-tissue	Pritchard

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	chr1:62661200-62667800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
3	chr1:62661600-62669000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:62662000-62666600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
5	chr1:62663800-62669000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:62664000-62667400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:62664000-62668400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:62664000-62668400	Weak transcription	Fetal Stomach	stomach
9	chr1:62664000-62673000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:62664400-62668600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:62664400-62668800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:62664600-62669800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:62664800-62668400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:62664800-62668800	Weak transcription	Fetal Lung	lung
15	chr1:62664800-62677800	Weak transcription	Placenta	Placenta
16	chr1:62665200-62672400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:62665400-62669600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:62665600-62668000	Weak transcription	HepG2	liver
19	chr1:62665600-62668400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:62665800-62666800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:62665800-62666800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:62665800-62670400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:62666000-62666800	Genic enhancers	H1 Cell Line	embryonic stem cell
24	chr1:62666000-62667000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:62666000-62695400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:62666200-62667000	Genic enhancers	H9 Cell Line	embryonic stem cell
27	chr1:62666400-62667600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
28	chr1:62666400-62667600	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr1:62666400-62668200	Genic enhancers	HUES64 Cell Line	embryonic stem cell

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