Variant report

Variant	rs3214072
Chromosome Location	chr9:100069900-100069901
allele	A/G
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	POLR2A	chr9:100069232-100070088	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD1	chr9:100069694-100070000	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr9:100069288-100069907	H1-hESC	embryonic stem cell:	n/a	chr9:100069499-100069508 chr9:100069499-100069508 chr9:100069499-100069508 chr9:100069501-100069510 chr9:100069555-100069565 chr9:100069588-100069597
4	CTCF	chr9:100069780-100069930	HRE	kidney:	n/a	n/a
5	POLR2A	chr9:100069009-100070004	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
CCDC180	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10122063	0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs10125198	0.96[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1037948	0.85[ASN][1000 genomes]
rs10435867	0.85[ASN][1000 genomes]
rs10435868	0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10448274	0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10759624	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10817487	0.83[ASN][1000 genomes]
rs10981280	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs10981288	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs10981296	0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs10981329	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs10981438	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10981890	0.87[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs11581	0.91[JPT][hapmap]
rs11791310	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs11998999	0.82[EUR][1000 genomes]
rs12004930	0.84[EUR][1000 genomes]
rs12005128	0.85[EUR][1000 genomes]
rs12235305	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13297670	0.82[EUR][1000 genomes]
rs13298346	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs13299627	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13301357	0.89[EUR][1000 genomes]
rs13302699	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1544203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1903635	0.86[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1947717	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2169456	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2219664	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242187	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2279114	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2306097	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2493442	0.82[CHB][hapmap];0.82[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2493443	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2502644	0.82[CHB][hapmap];0.94[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2615143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2615145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2795365	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2795367	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2818238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2818239	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2818243	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34382632	0.83[EUR][1000 genomes]
rs34955252	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35609998	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3747489	0.96[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs3747493	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3747496	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3802471	0.85[ASN][1000 genomes]
rs4237189	0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4284138	0.87[EUR][1000 genomes]
rs4313271	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4366181	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4523384	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4523385	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs4554595	0.86[ASN][1000 genomes]
rs4743072	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743076	0.96[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[ASN][1000 genomes]
rs4743077	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[ASN][1000 genomes]
rs4743084	0.96[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs55694850	0.82[EUR][1000 genomes]
rs6478095	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6478131	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7020393	0.86[JPT][hapmap]
rs7042707	0.87[JPT][hapmap]
rs713066	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72747776	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7470446	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs750674	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7856924	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7859665	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs9696167	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3214072	VN1R51P	cis	Thyroid	GTEx
rs3214072	ANKRD18CP	cis	Thyroid	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100057000-100075000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr9:100057400-100075400	Weak transcription	Dnd41	blood
3	chr9:100060200-100071600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:100068800-100071600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:100068800-100074200	Weak transcription	Thymus	Thymus
6	chr9:100069000-100070000	Flanking Active TSS	Brain Anterior Caudate	brain
7	chr9:100069000-100070000	Flanking Active TSS	Brain Hippocampus Middle	brain
8	chr9:100069000-100070200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr9:100069000-100070200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:100069000-100070400	Flanking Active TSS	Brain Cingulate Gyrus	brain
11	chr9:100069000-100070400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
12	chr9:100069000-100070400	Flanking Active TSS	Osteobl	bone
13	chr9:100069200-100070000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:100069200-100070000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr9:100069200-100070000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr9:100069200-100070000	Flanking Active TSS	Brain Substantia Nigra	brain
17	chr9:100069200-100070000	Active TSS	Fetal Kidney	kidney
18	chr9:100069200-100070000	Bivalent Enhancer	Stomach Mucosa	stomach
19	chr9:100069200-100070200	Active TSS	Muscle Satellite Cultured Cells	--
20	chr9:100069200-100070200	Flanking Active TSS	Brain Angular Gyrus	brain
21	chr9:100069200-100070200	Bivalent Enhancer	Fetal Brain Male	brain
22	chr9:100069200-100070200	Flanking Bivalent TSS/Enh	Fetal Lung	lung
23	chr9:100069200-100070200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr9:100069200-100070200	Flanking Active TSS	NH-A	brain
25	chr9:100069200-100070400	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr9:100069200-100070400	Flanking Active TSS	Ovary	ovary
27	chr9:100069200-100070400	Enhancers	Pancreas	Pancrea
28	chr9:100069200-100070600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:100069200-100071800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr9:100069400-100070000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:100069400-100070000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr9:100069400-100070000	Enhancers	Fetal Heart	heart
33	chr9:100069400-100070000	Active TSS	Psoas Muscle	Psoas
34	chr9:100069400-100070200	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr9:100069400-100070200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:100069400-100070200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:100069400-100070200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
38	chr9:100069400-100070200	Bivalent Enhancer	Fetal Thymus	thymus
39	chr9:100069400-100070200	Enhancers	Lung	lung
40	chr9:100069400-100070200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr9:100069400-100070200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
42	chr9:100069400-100070400	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr9:100069400-100070400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:100069400-100070400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:100069400-100070400	Enhancers	Esophagus	oesophagus
46	chr9:100069400-100070400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
47	chr9:100069400-100070400	Enhancers	Gastric	stomach
48	chr9:100069400-100071600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:100069400-100092800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr9:100069600-100070000	Active TSS	iPS-18 Cell Line	embryonic stem cell

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