Variant report

Variant	rs10889296
Chromosome Location	chr1:62663868-62663869
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1112561	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11207918	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11207919	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11207932	1.00[CEU][hapmap]
rs11207936	1.00[CEU][hapmap]
rs11802658	1.00[CEU][hapmap]
rs11805853	1.00[CEU][hapmap]
rs12116810	0.97[ASN][1000 genomes]
rs12120440	0.95[ASN][1000 genomes]
rs12133047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2366313	0.95[ASN][1000 genomes]
rs2366314	0.92[ASN][1000 genomes]
rs2366315	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41514144	1.00[CEU][hapmap]
rs7551777	1.00[CEU][hapmap]

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
rs10889296	L1TD1	cis	Thyroid	GTEx

Chromatin state (count:38 , 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	chr1:62661000-62675600	Weak transcription	Right Atrium	heart
3	chr1:62661200-62667800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
4	chr1:62661600-62669000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:62661800-62664000	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
6	chr1:62661800-62666400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
7	chr1:62662000-62664000	Transcr. at gene 5' and 3'	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:62662000-62665800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
9	chr1:62662000-62666000	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
10	chr1:62662000-62666400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
11	chr1:62662000-62666600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
12	chr1:62662200-62664000	Weak transcription	Fetal Lung	lung
13	chr1:62662200-62664400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:62662400-62664000	Enhancers	Placenta Amnion	Placenta Amnion
15	chr1:62662400-62665800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:62662600-62664000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:62663000-62664000	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:62663200-62664000	Enhancers	Placenta	Placenta
19	chr1:62663400-62664000	Enhancers	Fetal Muscle Trunk	muscle
20	chr1:62663400-62664000	Strong transcription	Fetal Stomach	stomach
21	chr1:62663600-62664000	Active TSS	Colonic Mucosa	Colon
22	chr1:62663600-62664200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:62663600-62664200	Enhancers	HepG2	liver
24	chr1:62663600-62664400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:62663600-62664600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr1:62663600-62664800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:62663800-62664000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
28	chr1:62663800-62664000	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr1:62663800-62664000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
30	chr1:62663800-62664000	Bivalent Enhancer	Fetal Heart	heart
31	chr1:62663800-62664000	Enhancers	Fetal Kidney	kidney
32	chr1:62663800-62664000	Enhancers	Pancreas	Pancrea
33	chr1:62663800-62664000	Enhancers	Right Ventricle	heart
34	chr1:62663800-62664400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:62663800-62664400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:62663800-62664600	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr1:62663800-62665600	Enhancers	Liver	Liver
38	chr1:62663800-62669000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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