Variant report

Variant	rs2669396
Chromosome Location	chr3:145852988-145852989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145851329..145855768-chr3:145877369..145881953,7	MCF-7	breast:
2	chr3:145851729..145854083-chr3:145855117..145857839,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs12171294	0.98[ASN][1000 genomes]
rs12496198	0.97[ASN][1000 genomes]
rs12496358	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12695808	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13063887	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13088158	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1349214	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1349215	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1375581	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1375582	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1375584	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1375587	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1449440	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1449441	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1449444	0.86[ASN][1000 genomes]
rs1449445	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1449450	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1449451	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1512900	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1512901	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1530741	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562699	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1613698	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1613796	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1707465	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1707466	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1707471	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1707472	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1707473	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1707479	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1900926	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2029137	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2029138	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2197908	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2305274	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2864792	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2864793	0.97[ASN][1000 genomes]
rs35399421	0.91[ASN][1000 genomes]
rs3762691	0.92[ASN][1000 genomes]
rs3792339	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792341	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3804660	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3804661	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3804664	0.84[ASN][1000 genomes]
rs3804665	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3804666	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3804668	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3804669	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3804670	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3816399	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3828381	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4681111	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4681112	0.85[ASN][1000 genomes]
rs4681113	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4681294	0.84[ASN][1000 genomes]
rs4681299	0.97[ASN][1000 genomes]
rs6440415	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6440417	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440419	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6710	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6783601	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6793380	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6799720	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6800294	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6800434	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6801418	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6802384	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7431590	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7614409	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7617913	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7639592	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7641322	0.91[ASN][1000 genomes]
rs764755	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs895929	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs895930	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9289712	0.85[ASN][1000 genomes]
rs9289713	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289714	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289715	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289716	0.92[ASN][1000 genomes]
rs9289717	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9289718	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs959329	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs963591	0.85[ASN][1000 genomes]
rs9809099	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9813047	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9822426	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9828112	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9836521	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9842036	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9842560	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9852153	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9852725	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9858081	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9858095	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9862005	0.84[ASN][1000 genomes]
rs9862237	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9865802	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9874388	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9877411	0.97[ASN][1000 genomes]
rs9878166	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9881251	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9882583	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv877613	chr3:145833232-145912055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2669396	PLOD2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145827000-145855200	Weak transcription	Aorta	Aorta
2	chr3:145832000-145870800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:145835800-145874000	Weak transcription	Psoas Muscle	Psoas
4	chr3:145840400-145874000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr3:145843600-145855200	Weak transcription	Left Ventricle	heart
6	chr3:145843600-145861200	Weak transcription	Right Ventricle	heart
7	chr3:145844600-145856000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:145844600-145860600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:145848000-145856800	Weak transcription	Fetal Intestine Small	intestine
10	chr3:145849800-145853000	Enhancers	Liver	Liver
11	chr3:145850000-145854400	Enhancers	Osteobl	bone
12	chr3:145850200-145853800	Enhancers	HepG2	liver
13	chr3:145850200-145856200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:145850200-145857600	Weak transcription	NHLF	lung
15	chr3:145850400-145860200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:145850400-145864400	Weak transcription	HMEC	breast
17	chr3:145851000-145853000	Enhancers	Fetal Heart	heart
18	chr3:145851200-145853000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:145851200-145853000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:145851200-145853000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:145851200-145853000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr3:145851200-145853000	Enhancers	Fetal Kidney	kidney
23	chr3:145851200-145853000	Enhancers	Rectal Smooth Muscle	rectum
24	chr3:145851200-145853000	Genic enhancers	HSMM	muscle
25	chr3:145851200-145853600	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr3:145851400-145853000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:145851400-145857600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:145851600-145853000	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr3:145851600-145853200	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr3:145851600-145853200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:145851600-145856000	Weak transcription	Ovary	ovary
32	chr3:145851600-145857400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:145851600-145860400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:145851600-145864200	Weak transcription	Right Atrium	heart
35	chr3:145851800-145853000	Enhancers	Colon Smooth Muscle	Colon
36	chr3:145851800-145854800	Enhancers	A549	lung
37	chr3:145851800-145856800	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:145851800-145857600	Weak transcription	HUVEC	blood vessel
39	chr3:145852000-145853000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:145852200-145857600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:145852400-145853000	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr3:145852400-145853000	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr3:145852400-145857800	Weak transcription	Fetal Intestine Large	intestine
44	chr3:145852600-145853000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr3:145852600-145853000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:145852600-145853000	Enhancers	Placenta Amnion	Placenta Amnion
47	chr3:145852600-145855800	Weak transcription	Fetal Stomach	stomach
48	chr3:145852600-145856800	Weak transcription	Brain Anterior Caudate	brain
49	chr3:145852600-145857400	Weak transcription	HSMMtube	muscle
50	chr3:145852600-145858000	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links