Variant report

Variant	rs1039142
Chromosome Location	chr18:30294510-30294511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:30294211..30294986-chr18:30781366..30782176,2	MCF-7	breast:
2	chr18:30262728..30263606-chr18:30294291..30295005,2	MCF-7	breast:
3	chr18:30294270..30295293-chr18:30499582..30500548,5	MCF-7	breast:
4	chr18:30294450..30295198-chr18:30499539..30500758,7	MCF-7	breast:

Extended variants
information (count: 142 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1039143	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10502605	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10502606	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10502607	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11081779	0.85[CEU][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12454261	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12454337	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12454409	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12456916	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12456996	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12457924	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12457977	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12953998	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954299	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956176	0.81[ASN][1000 genomes]
rs12956194	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12956370	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12956427	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12956607	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957691	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12959986	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12960282	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12961920	1.00[CEU][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]
rs12964622	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12967142	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12967667	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12967862	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12968405	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12968480	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12969530	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12969622	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12969651	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12969727	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12969760	0.88[EUR][1000 genomes]
rs12969787	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12969799	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12970122	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12970129	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12970312	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12970723	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12970991	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12971179	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1357535	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1357536	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1357538	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1403760	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1403761	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1403762	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1523579	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1523591	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1523592	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17665504	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17665516	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17665734	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17665806	0.81[EUR][1000 genomes]
rs1851700	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1880113	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2030622	1.00[CEU][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2049335	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049336	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132819	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2140447	1.00[CEU][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2140448	0.95[CEU][hapmap];0.99[EUR][1000 genomes]
rs2140449	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2173180	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2421641	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs4597394	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55962103	0.81[ASN][1000 genomes]
rs6506979	0.91[EUR][1000 genomes]
rs6506980	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs6506982	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6506983	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6506984	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6506985	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6506986	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs689523	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs689525	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7228647	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7228954	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7230048	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7230052	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7230438	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7230625	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7232695	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7233023	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7233463	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7234525	0.91[CEU][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7234772	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7236408	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7237843	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7239898	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7241764	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7242010	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8083192	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8089651	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8098984	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8099131	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8099133	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8099299	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9646509	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9945156	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9946368	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9946664	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9951265	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9951538	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9952507	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs9952882	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9953014	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9953107	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9953121	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9953954	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9953972	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9953979	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9954196	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9954483	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9954691	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9954988	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9954999	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9955000	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9955063	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9955106	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9957809	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9957814	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9958329	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9962132	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9963102	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9963370	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9963435	1.00[CEU][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9965787	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9965869	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9966576	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060732	chr18:30267156-30304435	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1062187	chr18:30267156-30306081	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1056335	chr18:30267904-30305840	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1059928	chr18:30267904-30306081	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1062522	chr18:30268383-30306081	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1057063	chr18:30280311-30304435	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1065587	chr18:30280311-30306081	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1067005	chr18:30290885-30304435	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1066471	chr18:30290885-30305840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1062670	chr18:30290885-30306081	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv998622	chr18:30293281-30304579	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:30288400-30299400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr18:30294000-30295200	Enhancers	Dnd41	blood
3	chr18:30294200-30294800	Enhancers	Primary B cells from cord blood	blood
4	chr18:30294200-30294800	Enhancers	Primary B cells from peripheral blood	blood
5	chr18:30294200-30295400	Enhancers	HepG2	liver
6	chr18:30294400-30294600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr18:30294400-30294600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr18:30294400-30295000	Enhancers	HUES64 Cell Line	embryonic stem cell

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