Variant report

Variant	rs2481707
Chromosome Location	chr1:62660669-62660670
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12137088	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12737213	0.96[EUR][1000 genomes]
rs2457822	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2481697	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2481698	0.83[EUR][1000 genomes]
rs2481708	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2941681	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2989009	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6656763	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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
rs2481707	L1TD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62659800-62661200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:62659800-62661800	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr1:62660000-62661000	Bivalent/Poised TSS	Psoas Muscle	Psoas
4	chr1:62660000-62661600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:62660000-62661800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr1:62660000-62662000	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:62660000-62662000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr1:62660000-62662000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:62660000-62662400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:62660000-62662600	Active TSS	Colonic Mucosa	Colon
11	chr1:62660000-62665200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:62660200-62660800	Active TSS	Fetal Lung	lung
13	chr1:62660200-62660800	Bivalent/Poised TSS	Fetal Stomach	stomach
14	chr1:62660200-62661000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:62660200-62661000	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr1:62660200-62661000	ZNF genes & repeats	Spleen	Spleen
17	chr1:62660200-62661200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:62660200-62661200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
19	chr1:62660200-62661400	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr1:62660200-62662000	Active TSS	H1 Cell Line	embryonic stem cell
21	chr1:62660200-62662000	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr1:62660200-62662000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:62660400-62660800	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr1:62660400-62660800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:62660400-62660800	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
26	chr1:62660400-62660800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
27	chr1:62660400-62660800	Bivalent Enhancer	NH-A	brain
28	chr1:62660400-62661000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr1:62660400-62661000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:62660400-62661000	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
31	chr1:62660400-62661000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:62660400-62661000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:62660400-62661000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
34	chr1:62660400-62661000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
35	chr1:62660400-62661000	Enhancers	Fetal Heart	heart
36	chr1:62660400-62661000	Flanking Active TSS	Placenta	Placenta
37	chr1:62660400-62661000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
38	chr1:62660400-62661200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
39	chr1:62660400-62661200	Bivalent Enhancer	Adipose Nuclei	Adipose
40	chr1:62660400-62661200	Bivalent/Poised TSS	Thymus	Thymus
41	chr1:62660400-62661200	Bivalent/Poised TSS	NHEK	skin
42	chr1:62660400-62661400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
43	chr1:62660400-62661600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:62660400-62661800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:62660400-62661800	Bivalent/Poised TSS	Fetal Kidney	kidney
46	chr1:62660400-62662000	Active TSS	Placenta Amnion	Placenta Amnion
47	chr1:62660400-62662600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:62660600-62660800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
49	chr1:62660600-62660800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:62660600-62660800	Bivalent Enhancer	Brain Hippocampus Middle	brain

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