Variant report

Variant	rs16880440
Chromosome Location	chr4:28280170-28280171
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:28278989..28281392-chr4:28295542..28298353,2	MCF-7	breast:
2	chr4:28279196..28281864-chr4:28281921..28283988,2	MCF-7	breast:

Extended variants
information (count: 144 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10011359	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10021592	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10049536	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10433806	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10433807	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10433842	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11932229	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11932359	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11940328	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12641399	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12642302	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12644493	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12645652	0.81[ASN][1000 genomes]
rs12646312	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12647447	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13123999	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1353650	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1353653	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1391219	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1497697	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1497699	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1497701	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1497712	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1497713	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1497716	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1497717	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16880483	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17619774	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17619834	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17681493	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17681723	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1846123	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1909051	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1948610	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2036181	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036182	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036183	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2309718	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2309722	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28377207	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28393792	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28413790	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28467171	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28491807	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28497932	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28513496	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28683509	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2871315	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28859954	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28889732	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35621260	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3924715	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4364251	0.87[AMR][1000 genomes]
rs4411974	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4435736	0.92[ASN][1000 genomes]
rs4464553	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4484281	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4550915	0.83[AMR][1000 genomes]
rs4616738	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4692049	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4692050	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4692301	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4692306	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4692307	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55869481	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56691107	0.85[ASN][1000 genomes]
rs57209669	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57457365	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58122848	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58189113	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60385254	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60551952	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60552601	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66505524	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66516862	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66538132	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66761305	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66953666	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67049612	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67152745	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67357525	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67568650	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67575578	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67596549	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67721098	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67773111	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67985929	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68027003	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68152757	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6815427	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68193608	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6830652	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6832858	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6833026	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6839474	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839502	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6852577	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73221856	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73221861	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73221862	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73221863	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73221864	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73221867	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73221869	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73221870	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73221871	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73221872	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73221875	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73221879	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73221881	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73221886	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73221887	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73221888	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73221889	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73221892	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73221899	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73221900	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7436389	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7661121	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7686001	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7698910	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs924236	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs924237	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs924238	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs924239	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs924240	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs964693	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs964694	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs964695	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs996281	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs996282	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9997640	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9999649	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[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	nsv1005382	chr4:28157180-28403800	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv878775	chr4:28163856-28473048	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1000514	chr4:28192982-28445194	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv878777	chr4:28208093-28343903	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv878778	chr4:28237783-28343903	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1012210	chr4:28246489-28419673	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv878779	chr4:28264394-28343903	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv967981	chr4:28272442-28281577	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1010133	chr4:28273244-28642942	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv878780	chr4:28273999-28341254	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1014938	chr4:28277683-28642942	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:28278600-28280200	Weak transcription	Brain Substantia Nigra	brain
2	chr4:28279000-28280200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:28279200-28282600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:28279400-28280600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:28279400-28282400	Enhancers	NHEK	skin
6	chr4:28279600-28280400	Enhancers	Stomach Mucosa	stomach
7	chr4:28279600-28280400	Enhancers	HSMM	muscle
8	chr4:28279600-28281400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:28279600-28282000	Enhancers	Brain Hippocampus Middle	brain
10	chr4:28279600-28282000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr4:28279600-28282200	Enhancers	HMEC	breast
12	chr4:28279600-28282400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:28279600-28282600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:28279800-28280800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr4:28279800-28281000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:28279800-28281800	Enhancers	Brain Cingulate Gyrus	brain
17	chr4:28280000-28280200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
18	chr4:28280000-28280600	Enhancers	Brain Angular Gyrus	brain
19	chr4:28280000-28282600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:28280000-28282600	Enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links