Variant report

Variant	rs963591
Chromosome Location	chr3:145793825-145793826
allele	A/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	POLR2A	chr3:145793622-145794454	U87	brain:	n/a	n/a
2	POLR2A	chr3:145793622-145794403	U87	brain:	n/a	n/a

Variant related genes	Relation type
PLOD2	TF binding region

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs12171294	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12496198	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12496358	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12695808	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13063887	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13088158	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1349214	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1349215	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1375578	0.81[EUR][1000 genomes]
rs1375581	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375582	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375584	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375587	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449438	0.81[EUR][1000 genomes]
rs1449439	0.81[EUR][1000 genomes]
rs1449440	0.92[ASN][1000 genomes]
rs1449441	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1449444	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449445	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449450	0.88[ASN][1000 genomes]
rs1449451	0.86[ASN][1000 genomes]
rs1512900	0.86[ASN][1000 genomes]
rs1512901	0.86[ASN][1000 genomes]
rs1530741	0.85[ASN][1000 genomes]
rs1562699	0.87[ASN][1000 genomes]
rs1584489	0.81[EUR][1000 genomes]
rs1613698	0.88[ASN][1000 genomes]
rs1613796	0.88[ASN][1000 genomes]
rs1707465	0.86[ASN][1000 genomes]
rs1707466	0.86[ASN][1000 genomes]
rs1707471	0.85[ASN][1000 genomes]
rs1707472	0.85[ASN][1000 genomes]
rs1707473	0.85[ASN][1000 genomes]
rs1707479	0.86[ASN][1000 genomes]
rs1900926	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2029137	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2029138	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2197908	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305274	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2669396	0.85[ASN][1000 genomes]
rs2864792	0.90[ASN][1000 genomes]
rs2864793	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35399421	0.84[EUR][1000 genomes]
rs3762691	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3792339	0.87[ASN][1000 genomes]
rs3792341	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804660	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3804661	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3804664	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804665	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804666	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804668	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804669	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804670	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3816399	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3828381	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681111	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681112	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681113	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681294	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681299	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440415	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6440417	0.91[ASN][1000 genomes]
rs6440419	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6710	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770862	0.81[EUR][1000 genomes]
rs6783601	0.88[ASN][1000 genomes]
rs6799720	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6800294	0.88[ASN][1000 genomes]
rs6800434	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6801418	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6802384	0.88[ASN][1000 genomes]
rs7431590	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7614409	0.91[ASN][1000 genomes]
rs7617913	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639592	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7641322	0.88[EUR][1000 genomes]
rs764755	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7647911	0.80[EUR][1000 genomes]
rs895929	0.88[ASN][1000 genomes]
rs895930	0.88[ASN][1000 genomes]
rs9289712	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289713	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9289714	0.92[ASN][1000 genomes]
rs9289715	0.92[ASN][1000 genomes]
rs9289716	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289717	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289718	0.86[ASN][1000 genomes]
rs959329	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9809099	0.88[ASN][1000 genomes]
rs9813047	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9822426	0.88[ASN][1000 genomes]
rs9828112	0.92[ASN][1000 genomes]
rs9836521	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9842036	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9842560	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9849076	0.81[EUR][1000 genomes]
rs9852153	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9852725	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858081	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9858095	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9862005	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9862237	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9865802	0.92[ASN][1000 genomes]
rs9867807	0.81[EUR][1000 genomes]
rs9874388	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9874627	0.82[EUR][1000 genomes]
rs9877411	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9878166	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9881251	0.92[ASN][1000 genomes]
rs9882583	0.81[AMR][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

No data

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	chr3:145780800-145819800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:145781800-145831800	Weak transcription	Psoas Muscle	Psoas
9	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
10	chr3:145784000-145811800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:145784800-145794000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:145785200-145806400	Weak transcription	Colonic Mucosa	Colon
14	chr3:145785200-145819400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr3:145785400-145796800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:145785600-145798600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:145787000-145807200	Weak transcription	Fetal Lung	lung
18	chr3:145787200-145798400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:145787600-145798200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:145789200-145796000	Weak transcription	HMEC	breast
21	chr3:145789200-145830800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:145789800-145811000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:145790000-145808400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:145790000-145819800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:145790200-145797000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:145790200-145798000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:145790200-145818600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:145790200-145819400	Weak transcription	Left Ventricle	heart
29	chr3:145790400-145794200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:145790400-145843200	Weak transcription	Right Ventricle	heart
31	chr3:145790800-145794200	Weak transcription	NHLF	lung
32	chr3:145791200-145794800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:145791600-145794000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:145791600-145833800	Weak transcription	NHDF-Ad	bronchial
35	chr3:145792200-145812200	Strong transcription	HSMM	muscle
36	chr3:145792600-145795000	Strong transcription	NH-A	brain
37	chr3:145792600-145795400	Strong transcription	Osteobl	bone
38	chr3:145792600-145803600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:145792800-145795400	Weak transcription	Brain Angular Gyrus	brain
40	chr3:145793000-145795200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:145793000-145799800	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr3:145793200-145796000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:145793400-145794000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:145793600-145794600	Strong transcription	HUVEC	blood vessel
45	chr3:145793600-145799000	Strong transcription	HepG2	liver
46	chr3:145793800-145794200	ZNF genes & repeats	Brain Anterior Caudate	brain
47	chr3:145793800-145794400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:145793800-145794400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
49	chr3:145793800-145794400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:145793800-145794400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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