Variant report

Variant	rs2457824
Chromosome Location	chr1:62660090-62660091
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr1:62660037-62660688	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr1:62659796-62660703	H1-hESC	embryonic stem cell:	n/a	n/a
3	SP1	chr1:62660084-62660614	H1-hESC	embryonic stem cell:	n/a	chr1:62660328-62660338 chr1:62660327-62660338 chr1:62660483-62660495 chr1:62660327-62660339 chr1:62660329-62660338 chr1:62660327-62660339
4	SP1	chr1:62659997-62660697	H1-hESC	embryonic stem cell:	n/a	chr1:62660328-62660338 chr1:62660327-62660338 chr1:62660483-62660495 chr1:62660327-62660339 chr1:62660329-62660338 chr1:62660327-62660339
5	TBP	chr1:62660032-62661095	H1-hESC	embryonic stem cell:	n/a	n/a
6	YY1	chr1:62660052-62660639	H1-hESC	embryonic stem cell:	n/a	n/a
7	ATF2	chr1:62659860-62661088	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZNF143	chr1:62659883-62660553	H1-hESC	embryonic stem cell:	n/a	n/a
9	RXRA	chr1:62660051-62660496	H1-hESC	embryonic stem cell:	n/a	chr1:62660249-62660258
10	SP4	chr1:62660064-62660763	H1-hESC	embryonic stem cell:	n/a	chr1:62660327-62660338
11	JUND	chr1:62659880-62660627	H1-hESC	embryonic stem cell:	n/a	n/a
12	TAF1	chr1:62660042-62661132	H1-hESC	embryonic stem cell:	n/a	n/a
13	ATF2	chr1:62659848-62661221	H1-hESC	embryonic stem cell:	n/a	n/a
14	CHD2	chr1:62659964-62660578	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
L1TD1	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11207912	1.00[ASN][1000 genomes]
rs1123777	1.00[ASN][1000 genomes]
rs11584978	1.00[ASN][1000 genomes]
rs12072694	1.00[ASN][1000 genomes]
rs12072734	1.00[ASN][1000 genomes]
rs12091611	1.00[ASN][1000 genomes]
rs1537316	1.00[ASN][1000 genomes]
rs17122925	1.00[ASN][1000 genomes]
rs17122991	1.00[ASN][1000 genomes]
rs2457813	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457818	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41313250	1.00[ASN][1000 genomes]
rs4456123	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4915794	1.00[ASN][1000 genomes]
rs56689647	1.00[ASN][1000 genomes]
rs57178450	1.00[ASN][1000 genomes]
rs58604849	1.00[ASN][1000 genomes]
rs61775625	1.00[ASN][1000 genomes]
rs61775631	1.00[ASN][1000 genomes]
rs61775681	1.00[ASN][1000 genomes]
rs61775682	1.00[ASN][1000 genomes]
rs61777667	1.00[ASN][1000 genomes]
rs61777685	1.00[ASN][1000 genomes]
rs61777687	1.00[ASN][1000 genomes]
rs61777734	1.00[ASN][1000 genomes]
rs61777736	1.00[ASN][1000 genomes]
rs6587957	1.00[ASN][1000 genomes]
rs6697095	1.00[ASN][1000 genomes]
rs72919758	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72921841	1.00[ASN][1000 genomes]
rs7534748	1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2457824	L1TD1	Cis_1M	lymphoblastoid	RTeQTL
rs2457824	L1TD1	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62646600-62660400	Weak transcription	Right Atrium	heart
2	chr1:62652000-62660200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:62659800-62661200	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr1:62659800-62661800	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr1:62660000-62660200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
6	chr1:62660000-62660200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:62660000-62660200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr1:62660000-62660200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
9	chr1:62660000-62660200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:62660000-62660200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:62660000-62660400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr1:62660000-62660400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:62660000-62660400	Active TSS	Fetal Kidney	kidney
14	chr1:62660000-62660400	Enhancers	Placenta	Placenta
15	chr1:62660000-62660400	Enhancers	Placenta Amnion	Placenta Amnion
16	chr1:62660000-62660400	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
17	chr1:62660000-62661000	Bivalent/Poised TSS	Psoas Muscle	Psoas
18	chr1:62660000-62661600	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr1:62660000-62661800	Active TSS	H9 Cell Line	embryonic stem cell
20	chr1:62660000-62662000	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr1:62660000-62662000	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr1:62660000-62662000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:62660000-62662400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:62660000-62662600	Active TSS	Colonic Mucosa	Colon
25	chr1:62660000-62665200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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