Variant report

Variant	rs1489780
Chromosome Location	chr3:87842935-87842936
allele	C/T
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	RCOR1	chr3:87841622-87842992	K562	blood:	n/a	n/a
2	POLR2A	chr3:87841187-87843887	K562	blood:	n/a	n/a
3	POLR2A	chr3:87842425-87843905	K562	blood:	n/a	n/a
4	HCFC1	chr3:87841696-87842945	K562	blood:	n/a	n/a
5	ZNF384	chr3:87842658-87843075	K562	blood:	n/a	n/a
6	MAZ	chr3:87841272-87843038	K562	blood:	n/a	n/a
7	UBTF	chr3:87841143-87843623	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000239572	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12485486	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12488028	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489435	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13316021	0.82[ASN][1000 genomes]
rs1873209	0.90[ASN][1000 genomes]
rs1873210	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2046796	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2880695	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28872274	0.82[ASN][1000 genomes]
rs4630962	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859104	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55754932	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55788242	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55807523	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56125632	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56169023	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56386821	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67303034	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6779623	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7643136	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9867061	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv590918	chr3:87323334-87910931	Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv877142	chr3:87630433-87854277	Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv877143	chr3:87630433-87860130	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv877144	chr3:87691029-87845957	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv834756	chr3:87763793-87938179	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1009981	chr3:87821573-88003956	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv536634	chr3:87821573-88003956	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1489780	HTR1F	cis	Thyroid	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:87840400-87843800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr3:87840800-87844600	Active TSS	K562	blood
3	chr3:87841200-87843000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
4	chr3:87841200-87843000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr3:87841200-87843000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr3:87841200-87843000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr3:87841200-87843000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr3:87841200-87843400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:87841200-87843400	Active TSS	Fetal Kidney	kidney
10	chr3:87841200-87843400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
11	chr3:87841200-87843400	Bivalent/Poised TSS	NH-A	brain
12	chr3:87841200-87843600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
13	chr3:87841400-87843000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:87841400-87843000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr3:87841400-87843000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr3:87841400-87843000	Active TSS	Brain Anterior Caudate	brain
17	chr3:87841400-87843000	Bivalent/Poised TSS	A549	lung
18	chr3:87841800-87843000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
19	chr3:87841800-87843200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:87842000-87843000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
21	chr3:87842000-87846200	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr3:87842400-87843000	Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr3:87842400-87843000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
24	chr3:87842400-87843000	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:87842400-87843000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
26	chr3:87842600-87843000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
27	chr3:87842600-87843000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
28	chr3:87842600-87843000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:87842600-87843000	Bivalent Enhancer	Colon Smooth Muscle	Colon
30	chr3:87842600-87843000	Bivalent Enhancer	Fetal Stomach	stomach
31	chr3:87842600-87843000	Flanking Active TSS	Thymus	Thymus
32	chr3:87842600-87843400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
33	chr3:87842600-87843400	Bivalent/Poised TSS	NHDF-Ad	bronchial
34	chr3:87842600-87843600	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr3:87842600-87851000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:87842800-87843000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:87842800-87843000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
38	chr3:87842800-87843000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:87842800-87843000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:87842800-87843000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:87842800-87843000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:87842800-87843000	Bivalent Enhancer	Brain Germinal Matrix	brain
43	chr3:87842800-87843400	Bivalent/Poised TSS	Adipose Nuclei	Adipose
44	chr3:87842800-87843400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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