Variant report

Variant	rs13100614
Chromosome Location	chr3:159512943-159512944
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	chr3:159506660..159510516-chr3:159511737..159514255,3	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12629172	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12631468	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13064339	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13065938	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes]
rs13065987	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13066040	0.89[MEX][hapmap]
rs13066560	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13067050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13072356	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13075534	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13077427	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs13078322	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13080307	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13080768	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13085339	0.91[CEU][hapmap];0.89[CHB][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13088481	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13088959	0.91[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13100094	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs16830741	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16830748	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16830780	0.85[CEU][hapmap]
rs2076889	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2126142	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs2366405	0.85[CEU][hapmap]
rs34586932	0.90[ASN][1000 genomes]
rs34682429	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35035161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35165740	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35527279	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35792854	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3892994	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680522	0.89[ASN][1000 genomes]
rs56077320	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58755984	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61597037	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441272	0.90[CHB][hapmap];0.90[ASN][1000 genomes]
rs6792870	0.85[CEU][hapmap];0.89[MEX][hapmap]
rs71625413	0.97[AMR][1000 genomes]
rs7631400	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs9860588	0.85[CEU][hapmap]
rs9880487	0.85[CEU][hapmap];0.89[MEX][hapmap]
rs9884085	0.85[CEU][hapmap];0.89[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4084	chr3:159492488-159513251	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13100614	PUS3	trans	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159493600-159516200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:159502000-159522800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr3:159504000-159518600	Enhancers	Brain Hippocampus Middle	brain
4	chr3:159504200-159518400	Enhancers	Brain Substantia Nigra	brain
5	chr3:159505000-159515000	Enhancers	Brain Angular Gyrus	brain
6	chr3:159505600-159515600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:159506000-159518200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:159506200-159522600	Weak transcription	Fetal Kidney	kidney
9	chr3:159506400-159513200	Weak transcription	NHLF	lung
10	chr3:159506400-159513800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:159506400-159522400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:159506600-159514200	Weak transcription	Fetal Heart	heart
13	chr3:159506800-159513000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:159507000-159513600	Weak transcription	NH-A	brain
15	chr3:159508000-159513800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:159508000-159513800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:159508000-159514000	Weak transcription	HMEC	breast
18	chr3:159508600-159520600	Enhancers	Brain Cingulate Gyrus	brain
19	chr3:159509000-159516600	Weak transcription	Liver	Liver
20	chr3:159509200-159515000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:159509200-159516600	Weak transcription	HepG2	liver
22	chr3:159509400-159513600	Weak transcription	Lung	lung
23	chr3:159509400-159513800	Enhancers	Colon Smooth Muscle	Colon
24	chr3:159509400-159514000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:159509400-159515600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:159509400-159517200	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr3:159509600-159513800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:159509600-159514000	Weak transcription	NHEK	skin
29	chr3:159510200-159513000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:159510200-159513000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:159510200-159513000	Weak transcription	Osteobl	bone
32	chr3:159510200-159513800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:159510200-159513800	Weak transcription	HSMM	muscle
34	chr3:159510200-159516200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:159510800-159513600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:159511000-159513000	Weak transcription	Right Ventricle	heart
37	chr3:159511000-159514400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:159511800-159514000	Weak transcription	A549	lung
39	chr3:159512200-159514400	Enhancers	Aorta	Aorta
40	chr3:159512200-159515800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:159512200-159516200	Enhancers	Brain Anterior Caudate	brain
42	chr3:159512400-159513400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:159512400-159514000	Weak transcription	HUVEC	blood vessel
44	chr3:159512400-159514400	Enhancers	Left Ventricle	heart
45	chr3:159512400-159514400	Enhancers	Right Atrium	heart
46	chr3:159512400-159517600	Enhancers	Adipose Nuclei	Adipose
47	chr3:159512600-159513000	Enhancers	Fetal Stomach	stomach
48	chr3:159512600-159513400	Flanking Active TSS	Rectal Smooth Muscle	rectum
49	chr3:159512600-159513400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr3:159512600-159514400	Flanking Active TSS	Stomach Smooth Muscle	stomach

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