Variant report

Variant	rs500608
Chromosome Location	chr11:73963741-73963742
allele	A/C
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	chr11:73963369-73969941	A549	lung:	n/a	n/a

Variant related genes	Relation type
P4HA3	TF binding region
ENSG00000206913	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10898954	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs1614299	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1615115	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1726735	0.81[AFR][1000 genomes]
rs1726744	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1726746	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1726751	0.85[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs1726752	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1783537	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1790381	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1790398	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1790399	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs1790404	0.89[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2848559	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs3018184	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4453265	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs474280	1.00[ASW][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[YRI][hapmap]
rs474835	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs486577	1.00[ASW][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[YRI][hapmap]
rs490539	1.00[ASW][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[YRI][hapmap]
rs4944036	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap]
rs556134	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs575096	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs578057	0.82[CHB][hapmap]
rs627354	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6592545	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs6592551	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs826033	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs826039	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs826056	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs826061	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs826062	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.80[EUR][1000 genomes]
rs826066	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs500608	P4HA3	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73907400-73969200	Weak transcription	HUVEC	blood vessel
2	chr11:73936000-73968000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:73936200-73966600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr11:73936400-73967000	Strong transcription	HSMM	muscle
5	chr11:73936400-73967600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:73938800-73967400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:73941000-73967600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:73941000-73967800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:73945600-73966800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr11:73946600-73966600	Strong transcription	A549	lung
11	chr11:73949400-73964600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:73950400-73966600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr11:73952000-73966800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr11:73955000-73964000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr11:73955000-73965400	Strong transcription	Hela-S3	cervix
16	chr11:73955000-73967600	Strong transcription	Fetal Thymus	thymus
17	chr11:73955400-73964400	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr11:73955800-73966600	Strong transcription	Placenta	Placenta
19	chr11:73955800-73968800	Weak transcription	Stomach Mucosa	stomach
20	chr11:73956000-73967200	Strong transcription	HepG2	liver
21	chr11:73956600-73966200	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr11:73956600-73966200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr11:73956800-73966000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:73956800-73966200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:73956800-73966200	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:73956800-73966400	Strong transcription	Osteobl	bone
27	chr11:73956800-73966600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:73956800-73966600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr11:73956800-73966800	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr11:73956800-73967800	Strong transcription	Adipose Nuclei	Adipose
31	chr11:73957000-73965800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr11:73957000-73965800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr11:73957000-73966000	Strong transcription	Ovary	ovary
34	chr11:73957000-73966200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr11:73957000-73966200	Strong transcription	Fetal Intestine Large	intestine
36	chr11:73957000-73966400	Strong transcription	Primary T cells from cord blood	blood
37	chr11:73957000-73966400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:73957000-73966400	Strong transcription	Brain Germinal Matrix	brain
39	chr11:73957000-73966400	Strong transcription	Left Ventricle	heart
40	chr11:73957000-73966400	Strong transcription	Dnd41	blood
41	chr11:73957000-73966400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr11:73957000-73966600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr11:73957000-73966600	Strong transcription	Brain Anterior Caudate	brain
44	chr11:73957000-73966800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr11:73957000-73966800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr11:73957000-73967400	Strong transcription	HSMMtube	muscle
47	chr11:73957000-73967800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr11:73957000-73967800	Strong transcription	Fetal Muscle Leg	muscle
49	chr11:73957000-73967800	Strong transcription	Fetal Stomach	stomach
50	chr11:73957000-73968000	Strong transcription	Fetal Muscle Trunk	muscle

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