Variant report

Variant	rs7154841
Chromosome Location	chr14:72073422-72073423
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	chr14:72044562..72046264-chr14:72073210..72075565,2	MCF-7	breast:

Extended variants
information (count: 137 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs10135680	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10138557	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10139519	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1029570	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10483836	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10873246	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11848785	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1204995	1.00[LWK][hapmap]
rs12127	0.82[EUR][1000 genomes]
rs12433040	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12879243	0.89[EUR][1000 genomes]
rs12880188	0.95[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12880291	0.82[EUR][1000 genomes]
rs12880611	0.90[EUR][1000 genomes]
rs12881643	0.87[EUR][1000 genomes]
rs12881957	0.87[EUR][1000 genomes]
rs12885344	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12887261	0.82[EUR][1000 genomes]
rs12889866	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12892512	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12894016	0.89[EUR][1000 genomes]
rs12894478	0.86[EUR][1000 genomes]
rs12896900	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12896986	0.90[EUR][1000 genomes]
rs14030	0.82[EUR][1000 genomes]
rs17178206	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17178234	0.90[EUR][1000 genomes]
rs17178387	0.88[EUR][1000 genomes]
rs17767499	0.87[EUR][1000 genomes]
rs17767523	0.90[EUR][1000 genomes]
rs17767553	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs17767680	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17767686	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1859643	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1981588	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2108049	0.90[EUR][1000 genomes]
rs2108057	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2109276	0.90[EUR][1000 genomes]
rs2190240	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2214836	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2332638	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2332640	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2332641	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2877729	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs28859432	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs33994051	0.90[EUR][1000 genomes]
rs34057981	0.82[EUR][1000 genomes]
rs34169215	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34176710	0.88[EUR][1000 genomes]
rs34281934	0.88[EUR][1000 genomes]
rs34320622	0.90[EUR][1000 genomes]
rs34347034	0.89[EUR][1000 genomes]
rs34388001	0.82[EUR][1000 genomes]
rs34454371	0.89[EUR][1000 genomes]
rs34469007	0.90[EUR][1000 genomes]
rs34480562	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34524083	0.86[EUR][1000 genomes]
rs34528131	0.86[EUR][1000 genomes]
rs34748537	0.86[EUR][1000 genomes]
rs34991781	0.81[EUR][1000 genomes]
rs34993988	0.87[EUR][1000 genomes]
rs35051046	0.87[EUR][1000 genomes]
rs35231795	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35260692	0.86[EUR][1000 genomes]
rs35415083	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35468256	0.87[EUR][1000 genomes]
rs35589413	0.88[EUR][1000 genomes]
rs35609708	0.82[EUR][1000 genomes]
rs35613269	0.90[EUR][1000 genomes]
rs35620527	0.82[EUR][1000 genomes]
rs35625243	0.80[EUR][1000 genomes]
rs35680546	0.88[EUR][1000 genomes]
rs35760654	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35831373	0.81[EUR][1000 genomes]
rs35854505	0.87[EUR][1000 genomes]
rs35866366	0.81[EUR][1000 genomes]
rs35971049	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36052007	0.88[EUR][1000 genomes]
rs36072220	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36093218	0.88[EUR][1000 genomes]
rs3784062	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3784064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3784066	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3825719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4140797	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4319698	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4899398	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4902938	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4902941	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4902942	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55883127	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56180634	0.86[EUR][1000 genomes]
rs56407721	0.87[EUR][1000 genomes]
rs61989367	0.90[EUR][1000 genomes]
rs61989373	0.90[EUR][1000 genomes]
rs61989374	0.90[EUR][1000 genomes]
rs61989377	0.89[EUR][1000 genomes]
rs61989379	0.82[EUR][1000 genomes]
rs61989382	0.88[EUR][1000 genomes]
rs61989383	0.94[EUR][1000 genomes]
rs61989386	0.88[EUR][1000 genomes]
rs61989417	0.93[AFR][1000 genomes]
rs61991247	0.86[EUR][1000 genomes]
rs61991248	0.86[EUR][1000 genomes]
rs61991250	0.86[EUR][1000 genomes]
rs61991254	0.86[EUR][1000 genomes]
rs61991255	0.90[EUR][1000 genomes]
rs6574015	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6574016	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66645707	0.88[EUR][1000 genomes]
rs67489015	0.87[EUR][1000 genomes]
rs7140501	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7142343	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7144299	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7144829	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7145755	0.87[EUR][1000 genomes]
rs7147668	0.86[EUR][1000 genomes]
rs7148679	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7152674	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7154787	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7156313	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7156460	0.86[EUR][1000 genomes]
rs7157241	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs722633	0.90[EUR][1000 genomes]
rs725673	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs757850	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8003478	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8006300	0.91[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8008605	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8010616	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8013161	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8014349	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8017775	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9323561	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9672060	0.95[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7154841	PCNX	cis	parietal	SCAN
rs7154841	COQ6	cis	parietal	SCAN
rs7154841	SIPA1L1	cis	cerebellum	SCAN
rs7154841	SMOC1	cis	cerebellum	SCAN
rs7154841	PCNX	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72053400-72098800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:72055200-72087800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:72059000-72098600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr14:72059400-72088000	Weak transcription	NHLF	lung
5	chr14:72059800-72085600	Weak transcription	NH-A	brain
6	chr14:72059800-72087600	Weak transcription	Hela-S3	cervix
7	chr14:72062800-72074000	Weak transcription	Brain Substantia Nigra	brain
8	chr14:72063200-72087200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr14:72064800-72084800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr14:72064800-72085000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr14:72065000-72087200	Weak transcription	NHEK	skin
12	chr14:72065200-72085400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr14:72065400-72085600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr14:72065800-72085600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr14:72065800-72089600	Weak transcription	HSMMtube	muscle
16	chr14:72067400-72084600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr14:72067400-72084600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr14:72069400-72083800	Weak transcription	Primary B cells from cord blood	blood
19	chr14:72069800-72074400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr14:72071200-72074800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr14:72071400-72074200	Weak transcription	Osteobl	bone
22	chr14:72071400-72085400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr14:72072200-72074400	Enhancers	Primary T cells from cord blood	blood
24	chr14:72072200-72075200	Enhancers	Brain Anterior Caudate	brain
25	chr14:72072400-72073600	Enhancers	Fetal Heart	heart
26	chr14:72072400-72074000	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr14:72072400-72074400	Enhancers	Thymus	Thymus
28	chr14:72072400-72075000	Enhancers	Brain Angular Gyrus	brain
29	chr14:72072400-72075000	Enhancers	Fetal Thymus	thymus
30	chr14:72072600-72073600	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr14:72072600-72073600	Flanking Active TSS	Dnd41	blood
32	chr14:72072600-72087000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr14:72072600-72090600	Weak transcription	Fetal Intestine Large	intestine
34	chr14:72072600-72103600	Weak transcription	Left Ventricle	heart
35	chr14:72072800-72074600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr14:72072800-72087200	Weak transcription	Aorta	Aorta
37	chr14:72073200-72073800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr14:72073200-72073800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr14:72073200-72073800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr14:72073200-72073800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr14:72073200-72074400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr14:72073200-72074400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr14:72073200-72074600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr14:72073200-72075000	Flanking Active TSS	GM12878-XiMat	blood
45	chr14:72073200-72075200	Enhancers	Brain Hippocampus Middle	brain
46	chr14:72073200-72085400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr14:72073200-72085600	Weak transcription	HSMM	muscle
48	chr14:72073200-72087200	Weak transcription	Fetal Intestine Small	intestine
49	chr14:72073200-72087400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr14:72073200-72090600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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