Variant report

Variant	rs1873210
Chromosome Location	chr3:87842202-87842203
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12485486	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12488028	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12489435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1489779	0.87[YRI][hapmap]
rs1489780	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1873209	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2046796	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2880695	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4630962	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55754932	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55788242	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55807523	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56125632	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56169023	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56386821	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67303034	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6779623	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7643136	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867061	0.81[JPT][hapmap]

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
rs1873210	HTR1F	cis	Thyroid	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

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	chr3:87841000-87842600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
4	chr3:87841200-87842400	Active TSS	NHLF	lung
5	chr3:87841200-87842600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:87841200-87842600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:87841200-87842600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:87841200-87842800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:87841200-87842800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:87841200-87842800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
11	chr3:87841200-87843000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
12	chr3:87841200-87843000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr3:87841200-87843000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr3:87841200-87843000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr3:87841200-87843000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr3:87841200-87843400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr3:87841200-87843400	Active TSS	Fetal Kidney	kidney
18	chr3:87841200-87843400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
19	chr3:87841200-87843400	Bivalent/Poised TSS	NH-A	brain
20	chr3:87841200-87843600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
21	chr3:87841400-87842600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:87841400-87842600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
23	chr3:87841400-87842600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
24	chr3:87841400-87842600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
25	chr3:87841400-87842600	Active TSS	Thymus	Thymus
26	chr3:87841400-87842800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr3:87841400-87842800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
28	chr3:87841400-87842800	Active TSS	Ovary	ovary
29	chr3:87841400-87842800	Active TSS	Right Atrium	heart
30	chr3:87841400-87843000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:87841400-87843000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
32	chr3:87841400-87843000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr3:87841400-87843000	Active TSS	Brain Anterior Caudate	brain
34	chr3:87841400-87843000	Bivalent/Poised TSS	A549	lung
35	chr3:87841600-87842400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:87841600-87842400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:87841600-87842400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:87841600-87842600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:87841600-87842600	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
40	chr3:87841600-87842600	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr3:87841600-87842600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:87841600-87842600	Active TSS	NHDF-Ad	bronchial
43	chr3:87841600-87842800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:87841600-87842800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
45	chr3:87841600-87842800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
46	chr3:87841600-87842800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
47	chr3:87841600-87842800	Bivalent Enhancer	Fetal Brain Male	brain
48	chr3:87841600-87842800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
49	chr3:87841600-87842800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
50	chr3:87841600-87842800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum

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