Variant report

Variant	rs2941681
Chromosome Location	chr1:62662850-62662851
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12137088	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12737213	0.93[EUR][1000 genomes]
rs2457822	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2481697	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2481707	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2481708	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2989009	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6656763	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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
rs2941681	L1TD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62660000-62665200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:62661000-62663800	Weak transcription	Pancreas	Pancrea
3	chr1:62661000-62675600	Weak transcription	Right Atrium	heart
4	chr1:62661200-62667800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
5	chr1:62661600-62663800	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
6	chr1:62661600-62669000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:62661800-62664000	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
8	chr1:62661800-62666400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
9	chr1:62662000-62663000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
10	chr1:62662000-62663600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:62662000-62663600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:62662000-62663600	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:62662000-62664000	Transcr. at gene 5' and 3'	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:62662000-62665800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
15	chr1:62662000-62666000	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
16	chr1:62662000-62666400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
17	chr1:62662000-62666600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
18	chr1:62662200-62663200	Weak transcription	Placenta	Placenta
19	chr1:62662200-62663800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:62662200-62664000	Weak transcription	Fetal Lung	lung
21	chr1:62662200-62664400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:62662400-62664000	Enhancers	Placenta Amnion	Placenta Amnion
23	chr1:62662400-62665800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:62662600-62663400	Weak transcription	Colonic Mucosa	Colon
25	chr1:62662600-62664000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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