Variant report

Variant	rs2029138
Chromosome Location	chr3:145793411-145793412
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	chr3:145792832-145793446	U87	brain:	n/a	n/a
2	POLR2A	chr3:145792447-145793452	U87	brain:	n/a	n/a

Variant related genes	Relation type
PLOD2	TF binding region

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs12171294	0.87[ASN][1000 genomes]
rs12496198	0.88[ASN][1000 genomes]
rs12496358	0.90[ASN][1000 genomes]
rs12695808	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13063887	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13088158	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1349214	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1349215	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1375581	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375582	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375584	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375587	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449440	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1449441	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449444	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449445	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449450	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1449451	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1512900	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1512901	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1530741	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1562699	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1613698	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1613796	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1707465	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1707466	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1707471	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1707472	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1707473	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1707479	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1900926	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2029137	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2197908	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305274	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2669396	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2864792	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2864793	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3762691	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3792339	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3792341	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804660	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3804661	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3804664	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804665	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804666	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804668	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804669	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804670	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3816399	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3828381	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681111	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681112	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681113	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681294	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681299	0.88[ASN][1000 genomes]
rs6440415	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6440417	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440419	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6710	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783601	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793380	0.82[EUR][1000 genomes]
rs6795690	0.83[EUR][1000 genomes]
rs6799720	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6800294	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6800434	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6801418	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6802384	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7431590	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7614409	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7617913	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639592	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs764755	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs895929	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs895930	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9289712	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289713	0.92[ASN][1000 genomes]
rs9289714	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9289715	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9289716	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9289717	0.91[ASN][1000 genomes]
rs9289718	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs959329	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs963591	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809099	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9813047	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9822426	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9828112	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9836521	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9842036	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9842560	0.88[ASN][1000 genomes]
rs9852153	0.92[ASN][1000 genomes]
rs9852725	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858081	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9858095	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9862005	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9862237	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9865802	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9874388	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9877411	0.88[ASN][1000 genomes]
rs9878166	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9881251	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9882583	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv965397	chr3:145789376-145797057	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2029138	PLOD2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145774600-145795400	Weak transcription	Aorta	Aorta
2	chr3:145777000-145819400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:145778200-145817200	Weak transcription	Fetal Stomach	stomach
4	chr3:145779600-145820600	Weak transcription	Fetal Kidney	kidney
5	chr3:145780000-145815600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:145780600-145820400	Weak transcription	Placenta	Placenta
7	chr3:145780800-145793800	Weak transcription	Ovary	ovary
8	chr3:145780800-145793800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:145780800-145819800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:145781800-145831800	Weak transcription	Psoas Muscle	Psoas
11	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
12	chr3:145784000-145811800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:145784800-145794000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:145785200-145806400	Weak transcription	Colonic Mucosa	Colon
16	chr3:145785200-145819400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:145785400-145796800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:145785600-145798600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:145786800-145793800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:145787000-145807200	Weak transcription	Fetal Lung	lung
21	chr3:145787200-145798400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:145787400-145793800	Weak transcription	Brain Anterior Caudate	brain
23	chr3:145787600-145798200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:145789200-145796000	Weak transcription	HMEC	breast
25	chr3:145789200-145830800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:145789400-145793800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:145789600-145793800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:145789800-145793800	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:145789800-145811000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:145790000-145808400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:145790000-145819800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:145790200-145793800	Weak transcription	Fetal Intestine Large	intestine
33	chr3:145790200-145793800	Weak transcription	HSMMtube	muscle
34	chr3:145790200-145797000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:145790200-145798000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:145790200-145818600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:145790200-145819400	Weak transcription	Left Ventricle	heart
38	chr3:145790400-145793800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:145790400-145794200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:145790400-145843200	Weak transcription	Right Ventricle	heart
41	chr3:145790600-145793800	Weak transcription	Adipose Nuclei	Adipose
42	chr3:145790600-145793800	Weak transcription	Liver	Liver
43	chr3:145790800-145793600	Weak transcription	HUVEC	blood vessel
44	chr3:145790800-145794200	Weak transcription	NHLF	lung
45	chr3:145791200-145794800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:145791600-145793800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:145791600-145794000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:145791600-145833800	Weak transcription	NHDF-Ad	bronchial
49	chr3:145791800-145793800	Weak transcription	Fetal Heart	heart
50	chr3:145792200-145812200	Strong transcription	HSMM	muscle

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