Variant report

Variant	rs13059754
Chromosome Location	chr3:99678490-99678491
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99665125..99667947-chr3:99677482..99680159,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10222474	0.86[CEU][hapmap]
rs10936008	0.82[TSI][hapmap]
rs11719468	0.84[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12488245	0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap]
rs1287284	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1384062	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1387647	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap]
rs16841874	0.84[CEU][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.81[MKK][hapmap]
rs1718235	0.84[CEU][hapmap];0.80[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.82[MKK][hapmap]
rs2130369	0.88[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap]
rs35422475	0.83[AMR][1000 genomes]
rs4577503	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4928150	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928151	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4928153	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap]
rs4928230	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.82[MKK][hapmap]
rs4928235	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4928237	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs58704213	0.82[ASN][1000 genomes]
rs6440967	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs6767441	0.92[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap]
rs6802817	0.83[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs6806323	0.83[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs704571	0.88[JPT][hapmap]
rs704572	0.92[JPT][hapmap]
rs704574	0.88[JPT][hapmap]
rs7613864	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7629487	0.92[CEU][hapmap]
rs7638900	0.82[TSI][hapmap]
rs7649349	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs7650727	0.84[CEU][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs766778	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs793437	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs793439	0.84[CEU][hapmap];0.80[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.82[MKK][hapmap]
rs793440	0.82[TSI][hapmap]
rs793443	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs793446	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs793456	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs793464	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs793470	0.82[TSI][hapmap]
rs793474	0.82[TSI][hapmap]
rs793475	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs793476	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs793483	0.88[JPT][hapmap]
rs793485	0.88[JPT][hapmap]
rs793497	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs793502	0.83[CEU][hapmap];0.80[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.82[MKK][hapmap]
rs793503	0.82[TSI][hapmap]
rs796976	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs796978	0.82[TSI][hapmap]
rs813218	0.84[CEU][hapmap];0.80[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.81[MKK][hapmap]
rs902159	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs923472	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs9289981	0.87[CEU][hapmap]
rs9811920	0.92[CEU][hapmap];0.85[GIH][hapmap];0.83[LWK][hapmap]
rs9837131	0.92[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13059754	EPHX1	trans	cerebellum	SCAN
rs13059754	C3orf26	Cis_1M	lymphoblastoid	RTeQTL
rs13059754	SENP7	cis	parietal	SCAN
rs13059754	OR5H6	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99657600-99686600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:99665000-99678800	Weak transcription	Aorta	Aorta
3	chr3:99669200-99679800	Weak transcription	Fetal Intestine Small	intestine
4	chr3:99670800-99679200	Weak transcription	Small Intestine	intestine
5	chr3:99671400-99679400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:99671600-99684200	Weak transcription	NHEK	skin
7	chr3:99671600-99688200	Weak transcription	Primary T cells from cord blood	blood
8	chr3:99672600-99680000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:99672800-99680000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:99673000-99679400	Weak transcription	Osteobl	bone
11	chr3:99673000-99680800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:99673000-99681000	Weak transcription	HSMM	muscle
13	chr3:99676200-99679200	Weak transcription	Stomach Mucosa	stomach
14	chr3:99676200-99679400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:99676400-99679400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:99676800-99679000	Weak transcription	HepG2	liver
17	chr3:99677200-99679400	Enhancers	Psoas Muscle	Psoas
18	chr3:99677400-99679200	Weak transcription	Fetal Kidney	kidney
19	chr3:99677400-99696600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:99677600-99679000	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:99677600-99679000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:99677600-99679200	Weak transcription	Adipose Nuclei	Adipose
23	chr3:99677600-99679200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:99677600-99679400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr3:99677600-99680200	Weak transcription	Fetal Heart	heart
26	chr3:99677600-99680400	Weak transcription	Left Ventricle	heart
27	chr3:99677600-99680800	Weak transcription	Right Ventricle	heart
28	chr3:99677600-99684400	Weak transcription	Fetal Stomach	stomach
29	chr3:99677600-99684400	Weak transcription	Pancreas	Pancrea
30	chr3:99677600-99684600	Weak transcription	Lung	lung
31	chr3:99677600-99692600	Weak transcription	Fetal Lung	lung
32	chr3:99677800-99679200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:99677800-99679200	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:99677800-99679200	Weak transcription	NHDF-Ad	bronchial
35	chr3:99677800-99680600	Weak transcription	HSMMtube	muscle
36	chr3:99677800-99680800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:99677800-99680800	Weak transcription	Right Atrium	heart
38	chr3:99678200-99680800	Weak transcription	Ovary	ovary
39	chr3:99678400-99678800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:99678400-99678800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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