Variant report

Variant	rs13084070
Chromosome Location	chr3:156859035-156859036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156855375..156857018-chr3:156858174..156860003,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LEKR1-5	chr3:156857264-156860654	NONHSAT092888

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10212545	0.82[EUR][1000 genomes]
rs10451871	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10451916	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1046938	0.81[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.80[ASN][1000 genomes]
rs10513507	0.92[CEU][hapmap]
rs1060543	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap]
rs11926167	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12629549	0.85[EUR][1000 genomes]
rs12637518	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12696045	0.82[ASN][1000 genomes]
rs13061214	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.80[ASN][1000 genomes]
rs13081036	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs13081038	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1392799	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1403104	0.81[CEU][hapmap];0.93[TSI][hapmap]
rs1500925	0.82[ASN][1000 genomes]
rs1587534	0.82[EUR][1000 genomes]
rs1587535	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs1608127	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs16827308	0.81[CEU][hapmap]
rs16827322	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs16827350	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2088814	0.85[EUR][1000 genomes]
rs2133952	0.85[EUR][1000 genomes]
rs35217153	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3749214	0.92[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap]
rs4368452	0.86[EUR][1000 genomes]
rs4383468	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4563363	0.87[EUR][1000 genomes]
rs4632503	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4680342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680344	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680346	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4680347	0.83[CEU][hapmap]
rs4680348	0.81[EUR][1000 genomes]
rs6441114	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441121	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs6441122	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441123	0.91[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs67196056	0.83[EUR][1000 genomes]
rs6767619	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6773061	0.82[ASN][1000 genomes]
rs6780831	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6781991	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789178	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6805114	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6808284	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6808457	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6809003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809394	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620178	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7625059	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs7636185	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7638194	0.81[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7642179	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7647643	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs924517	0.85[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs9289978	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9289979	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9811195	0.81[ASN][1000 genomes]
rs9827676	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9831830	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9838724	0.84[EUR][1000 genomes]
rs9848409	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849168	0.81[ASN][1000 genomes]
rs9858423	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9861469	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9867618	0.85[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][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	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
2	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv520331	chr3:156858300-156915650	Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13084070	PTX3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156848400-156866000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:156848400-156866000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:156848600-156876600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:156849000-156860000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:156849000-156861000	Weak transcription	Dnd41	blood
6	chr3:156849000-156861800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:156849000-156862400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:156849200-156861600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:156849200-156861600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:156849400-156861600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:156849800-156864000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:156850000-156860200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:156850400-156860800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:156850400-156861600	Weak transcription	Hela-S3	cervix
15	chr3:156851000-156861000	Weak transcription	HUVEC	blood vessel
16	chr3:156852600-156873400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr3:156853200-156865400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:156853400-156872000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr3:156854000-156861200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:156854200-156860200	Weak transcription	Thymus	Thymus
21	chr3:156854800-156860200	Weak transcription	Esophagus	oesophagus
22	chr3:156855000-156860000	Weak transcription	Right Ventricle	heart
23	chr3:156855000-156860200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:156855000-156865800	Weak transcription	Aorta	Aorta
25	chr3:156855000-156866000	Weak transcription	Ovary	ovary
26	chr3:156855000-156872000	Weak transcription	Right Atrium	heart
27	chr3:156855200-156860000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:156855200-156860200	Weak transcription	Small Intestine	intestine
29	chr3:156855200-156861600	Weak transcription	Psoas Muscle	Psoas
30	chr3:156855200-156861800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:156855200-156862000	Weak transcription	Pancreas	Pancrea
32	chr3:156855200-156862200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:156855400-156860000	Weak transcription	HSMM	muscle
34	chr3:156855400-156860200	Weak transcription	Spleen	Spleen
35	chr3:156855400-156860800	Weak transcription	GM12878-XiMat	blood
36	chr3:156855400-156862000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:156855400-156862200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:156855400-156862200	Weak transcription	HSMMtube	muscle
39	chr3:156855400-156865400	Weak transcription	Fetal Brain Male	brain
40	chr3:156855400-156865800	Weak transcription	Colonic Mucosa	Colon
41	chr3:156855400-156866000	Weak transcription	Fetal Heart	heart
42	chr3:156855400-156877000	Weak transcription	Gastric	stomach
43	chr3:156855600-156859200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:156855600-156859200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:156855600-156859200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:156855600-156859200	Weak transcription	Brain Hippocampus Middle	brain
47	chr3:156855600-156860000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:156855600-156860000	Weak transcription	Brain Substantia Nigra	brain
49	chr3:156855600-156860200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:156855600-156860200	Weak transcription	Brain Anterior Caudate	brain

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