Variant report

Variant	rs2457822
Chromosome Location	chr1:62661622-62661623
allele	A/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	0.90[EUR][1000 genomes]
rs12737213	0.91[EUR][1000 genomes]
rs2481697	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2481707	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2481708	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2941681	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2989009	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6656763	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.87[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
rs2457822	L1TD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62659800-62661800	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr1:62660000-62661800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr1:62660000-62662000	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr1:62660000-62662000	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr1:62660000-62662000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:62660000-62662400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:62660000-62662600	Active TSS	Colonic Mucosa	Colon
8	chr1:62660000-62665200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:62660200-62662000	Active TSS	H1 Cell Line	embryonic stem cell
10	chr1:62660200-62662000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr1:62660200-62662000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:62660400-62661800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:62660400-62661800	Bivalent/Poised TSS	Fetal Kidney	kidney
14	chr1:62660400-62662000	Active TSS	Placenta Amnion	Placenta Amnion
15	chr1:62660400-62662600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:62661000-62661800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:62661000-62662000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:62661000-62662200	Active TSS	Placenta	Placenta
19	chr1:62661000-62663800	Weak transcription	Pancreas	Pancrea
20	chr1:62661000-62675600	Weak transcription	Right Atrium	heart
21	chr1:62661200-62661800	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr1:62661200-62662000	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr1:62661200-62662200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:62661200-62667800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
25	chr1:62661400-62661800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr1:62661400-62662200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:62661600-62661800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
28	chr1:62661600-62662000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:62661600-62662000	Bivalent Enhancer	Fetal Stomach	stomach
30	chr1:62661600-62662200	Bivalent Enhancer	Fetal Muscle Leg	muscle
31	chr1:62661600-62663800	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
32	chr1:62661600-62669000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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