Variant report

Variant	rs12496198
Chromosome Location	chr3:145835383-145835384
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:145831639..145836013-chr3:145876068..145880595,7	MCF-7	breast:
2	chr3:145783644..145786560-chr3:145833867..145835451,2	MCF-7	breast:
3	chr3:145832668..145836066-chr3:145839232..145841565,3	MCF-7	breast:
4	chr3:145829569..145840903-chr3:145873254..145880972,31	MCF-7	breast:
5	chr3:145834823..145837112-chr3:145844959..145847874,2	MCF-7	breast:
6	chr3:145832179..145836696-chr3:145881447..145885871,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs12171294	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12496358	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12695808	0.97[ASN][1000 genomes]
rs13063887	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13088158	0.87[ASN][1000 genomes]
rs1349214	0.96[ASN][1000 genomes]
rs1349215	0.96[ASN][1000 genomes]
rs1355685	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1375581	0.86[ASN][1000 genomes]
rs1375582	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1375584	0.88[ASN][1000 genomes]
rs1375587	0.87[ASN][1000 genomes]
rs1449440	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1449441	0.81[CEU][hapmap];0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs1449444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1449445	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1449450	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1449451	0.97[ASN][1000 genomes]
rs1512900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1512901	0.98[ASN][1000 genomes]
rs1530741	0.97[ASN][1000 genomes]
rs1562699	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1613698	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1613796	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1707465	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1707466	0.99[ASN][1000 genomes]
rs1707471	0.97[ASN][1000 genomes]
rs1707472	0.97[ASN][1000 genomes]
rs1707473	0.97[ASN][1000 genomes]
rs1707479	0.99[ASN][1000 genomes]
rs1900926	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2029137	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2029138	0.88[ASN][1000 genomes]
rs2197908	0.87[ASN][1000 genomes]
rs2305274	0.88[ASN][1000 genomes]
rs2669396	0.97[ASN][1000 genomes]
rs2864792	0.92[ASN][1000 genomes]
rs2864793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35399421	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3762691	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3792339	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3792341	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3804660	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3804661	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3804664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3804665	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3804666	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3804668	0.88[ASN][1000 genomes]
rs3804669	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3804670	0.86[ASN][1000 genomes]
rs3816399	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3828381	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4681111	0.88[ASN][1000 genomes]
rs4681112	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4681113	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4681294	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440415	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6440417	0.95[ASN][1000 genomes]
rs6440419	0.96[ASN][1000 genomes]
rs6710	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6783601	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6793380	0.86[ASN][1000 genomes]
rs6799720	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800294	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6800434	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6801418	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6802384	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7431590	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7614409	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7617913	0.88[ASN][1000 genomes]
rs7639592	0.87[ASN][1000 genomes]
rs7641322	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7645622	0.91[CHB][hapmap]
rs764755	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs895929	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs895930	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9289712	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9289713	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289714	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9289715	0.84[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9289716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9289717	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9289718	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs959329	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs963591	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9809099	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9813047	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9822426	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9828112	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9836521	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9842036	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9842560	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852153	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9852725	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9858081	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858095	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862005	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9862237	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9865802	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9874388	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9877411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878166	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881251	0.94[ASN][1000 genomes]
rs9882583	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12496198	PLOD2	cis	Esophagus Mucosa	GTEx
rs12496198	PLOD2	cis	multi-tissue	Pritchard

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
2	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:145790400-145843200	Weak transcription	Right Ventricle	heart
4	chr3:145798800-145839200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:145810400-145849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:145810800-145851200	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:145812200-145839200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:145814200-145841000	Weak transcription	Lung	lung
9	chr3:145816000-145836800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:145816400-145842000	Weak transcription	Colonic Mucosa	Colon
11	chr3:145819800-145841800	Weak transcription	Fetal Heart	heart
12	chr3:145819800-145849200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:145821000-145849800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:145821200-145835400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:145822800-145836800	Weak transcription	Ovary	ovary
16	chr3:145824600-145839600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:145825000-145835400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:145827000-145855200	Weak transcription	Aorta	Aorta
19	chr3:145827400-145836600	Weak transcription	Adipose Nuclei	Adipose
20	chr3:145827400-145836600	Weak transcription	HSMMtube	muscle
21	chr3:145827400-145840200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:145827400-145842000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:145828600-145837200	Strong transcription	HSMM	muscle
24	chr3:145831400-145848400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:145832000-145836800	Weak transcription	Placenta	Placenta
26	chr3:145832000-145870800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:145832200-145835600	Weak transcription	Psoas Muscle	Psoas
28	chr3:145832200-145836800	Weak transcription	Left Ventricle	heart
29	chr3:145832200-145838400	Weak transcription	Fetal Stomach	stomach
30	chr3:145832400-145835400	Strong transcription	Osteobl	bone
31	chr3:145832600-145848400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:145833000-145835600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:145833000-145835600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
34	chr3:145833000-145837400	Strong transcription	HUVEC	blood vessel
35	chr3:145833200-145837200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:145833600-145843200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:145833800-145835400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:145834200-145835400	Weak transcription	Fetal Intestine Large	intestine
39	chr3:145834200-145836800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:145834200-145837200	Strong transcription	A549	lung
41	chr3:145834200-145851200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:145834400-145835400	Weak transcription	NH-A	brain
43	chr3:145834400-145839000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:145834400-145839600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:145834400-145851400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:145834600-145835600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:145834600-145835800	Weak transcription	Liver	Liver
48	chr3:145834600-145836600	Weak transcription	Fetal Lung	lung
49	chr3:145834600-145836600	Weak transcription	HepG2	liver
50	chr3:145834600-145837200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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