Variant report

Variant	rs12880188
Chromosome Location	chr14:72009745-72009746
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71785895..71788432-chr14:72008692..72011140,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197555	Chromatin interaction

Extended variants
information (count: 181 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:178)

rs_ID	r²[population]
rs10133626	1.00[JPT][hapmap]
rs10135680	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10138557	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10139519	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs1029570	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10483836	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873246	0.81[ASN][1000 genomes]
rs11848785	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1204995	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1204996	1.00[JPT][hapmap]
rs12127	0.84[EUR][1000 genomes]
rs12433040	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12878989	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12879243	0.89[EUR][1000 genomes]
rs12880291	0.84[EUR][1000 genomes]
rs12880611	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12881643	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12881957	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12885344	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12887261	0.84[EUR][1000 genomes]
rs12889866	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12892512	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12894016	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12894478	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12896900	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12896986	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs14030	0.84[EUR][1000 genomes]
rs17178045	0.80[EUR][1000 genomes]
rs17178206	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17178234	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17178387	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17767392	0.81[EUR][1000 genomes]
rs17767410	0.82[EUR][1000 genomes]
rs17767446	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17767499	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17767523	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17767553	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17767680	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767686	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859643	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1981588	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1990241	0.82[EUR][1000 genomes]
rs2108049	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2108057	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2108707	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2109276	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2190240	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2214836	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2286136	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs2332638	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2332640	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2332641	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2877729	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28859432	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33994051	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34011442	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34057981	0.83[EUR][1000 genomes]
rs34169215	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34176710	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34281934	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34320622	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34347034	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34388001	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34454371	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34469007	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34480562	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34524083	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34528013	0.81[EUR][1000 genomes]
rs34528131	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34533948	0.81[EUR][1000 genomes]
rs34649709	0.81[EUR][1000 genomes]
rs34674149	0.82[EUR][1000 genomes]
rs34725136	0.81[EUR][1000 genomes]
rs34748537	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34767050	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34873919	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34991781	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34993988	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35051046	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35054229	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35122644	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35231795	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35260692	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35415083	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35468256	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35589413	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35609708	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35613269	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35620527	0.84[EUR][1000 genomes]
rs35621718	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35625243	0.83[EUR][1000 genomes]
rs35680546	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35692397	0.80[EUR][1000 genomes]
rs35760654	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35796129	0.81[EUR][1000 genomes]
rs35822724	0.82[EUR][1000 genomes]
rs35831373	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35854505	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35866366	0.81[EUR][1000 genomes]
rs35971049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36052007	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36057816	0.81[EUR][1000 genomes]
rs36072220	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36093218	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3784062	0.93[EUR][1000 genomes]
rs3784064	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3784066	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825719	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4319698	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4899398	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4902938	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4902941	0.92[EUR][1000 genomes]
rs4902942	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55883127	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56180634	0.91[EUR][1000 genomes]
rs56363446	0.81[EUR][1000 genomes]
rs56407721	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61989367	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61989373	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61989374	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61989377	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61989379	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61989382	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61989383	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989386	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61991199	0.81[EUR][1000 genomes]
rs61991201	0.81[EUR][1000 genomes]
rs61991202	0.81[EUR][1000 genomes]
rs61991203	0.81[EUR][1000 genomes]
rs61991204	0.81[EUR][1000 genomes]
rs61991205	0.82[EUR][1000 genomes]
rs61991213	0.80[EUR][1000 genomes]
rs61991243	0.82[EUR][1000 genomes]
rs61991246	0.81[EUR][1000 genomes]
rs61991247	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61991248	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61991249	0.82[EUR][1000 genomes]
rs61991250	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61991254	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61991255	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6574015	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6574016	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66645707	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67489015	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68073803	0.81[EUR][1000 genomes]
rs7140354	0.81[EUR][1000 genomes]
rs7140501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7142180	0.81[EUR][1000 genomes]
rs7142343	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7144299	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7144829	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7145755	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7147434	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7147668	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7152674	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7152842	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs7154787	0.83[EUR][1000 genomes]
rs7154841	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7156313	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7156460	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7157241	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs722633	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs723966	0.81[EUR][1000 genomes]
rs725673	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72728427	0.82[EUR][1000 genomes]
rs757850	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8003478	0.86[EUR][1000 genomes]
rs8006300	0.95[CEU][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8007068	0.82[EUR][1000 genomes]
rs8008605	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8010616	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8013161	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8014349	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8015644	0.80[EUR][1000 genomes]
rs8017775	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8019721	0.82[EUR][1000 genomes]
rs9323561	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9672060	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv498021	chr14:71874708-72128721	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3398985	chr14:71927884-72404676	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3421223	chr14:72008599-72012997	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12880188	PCNX	cis	parietal	SCAN
rs12880188	SMOC1	cis	cerebellum	SCAN
rs12880188	PCNX	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71978400-72014800	Weak transcription	HMEC	breast
2	chr14:71980000-72021200	Weak transcription	Hela-S3	cervix
3	chr14:71981400-72021400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr14:71997800-72017600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr14:72001400-72009800	Enhancers	Fetal Heart	heart
6	chr14:72003000-72017800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr14:72006600-72019400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr14:72006600-72021800	Weak transcription	Small Intestine	intestine
9	chr14:72007000-72011200	Weak transcription	Right Ventricle	heart
10	chr14:72007200-72019600	Weak transcription	Primary B cells from cord blood	blood
11	chr14:72007200-72020200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr14:72007200-72021800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr14:72007400-72018200	Weak transcription	NHLF	lung
14	chr14:72007400-72020400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr14:72007600-72009800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr14:72007600-72010000	Weak transcription	Brain Anterior Caudate	brain
17	chr14:72007600-72012200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr14:72007600-72017400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr14:72007600-72017400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr14:72007800-72009800	Weak transcription	NHDF-Ad	bronchial
21	chr14:72007800-72016800	Weak transcription	Brain Hippocampus Middle	brain
22	chr14:72007800-72017200	Weak transcription	Osteobl	bone
23	chr14:72008400-72009800	Enhancers	Primary T cells from cord blood	blood
24	chr14:72008400-72017600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr14:72008400-72018200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr14:72008400-72018400	Weak transcription	Left Ventricle	heart
27	chr14:72008600-72009800	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr14:72009000-72015800	Weak transcription	GM12878-XiMat	blood
29	chr14:72009000-72017000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr14:72009200-72015400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr14:72009400-72009800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr14:72009400-72017000	Weak transcription	Spleen	Spleen
33	chr14:72009600-72017200	Weak transcription	HSMM	muscle

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