Variant report

Variant	rs7686001
Chromosome Location	chr4:28249931-28249932
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	chr4:28248668..28250669-chr4:28250991..28253691,2	MCF-7	breast:

Extended variants
information (count: 137 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10011359	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10021592	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10049536	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10433806	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10433807	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10433842	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11932229	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11932359	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11940328	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12641399	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12642302	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12644493	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12646312	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12647447	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13123999	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1353650	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1353653	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1391219	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1497697	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1497699	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1497701	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1497712	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1497713	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1497716	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1497717	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16880440	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16880483	0.90[EUR][1000 genomes]
rs17619774	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17619834	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17681493	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17681723	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1846123	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1909051	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1948610	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2036181	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036182	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036183	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2309718	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2309722	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28377207	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28393792	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28413790	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28467171	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28491807	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28497932	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28513496	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28683509	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2871315	0.86[EUR][1000 genomes]
rs28859954	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28889732	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35621260	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3924715	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4364251	0.80[EUR][1000 genomes]
rs4411974	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4435736	0.92[ASN][1000 genomes]
rs4464553	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4484281	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4616738	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4692049	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4692050	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4692301	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4692306	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4692307	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55869481	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56691107	0.94[ASN][1000 genomes]
rs57209669	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57457365	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58122848	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58189113	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60385254	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60551952	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60552601	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66505524	0.90[EUR][1000 genomes]
rs66516862	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66538132	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66761305	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66953666	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67049612	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67152745	0.88[EUR][1000 genomes]
rs67357525	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67568650	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67575578	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67596549	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67721098	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67773111	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67985929	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68027003	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68152757	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6815427	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68193608	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6830652	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6832858	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6833026	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6839474	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6839502	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6852577	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73221856	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73221861	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73221862	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73221863	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73221864	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73221867	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73221869	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73221870	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73221871	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73221872	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73221875	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73221879	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73221881	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73221886	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73221887	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73221888	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73221889	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73221892	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7436389	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7661121	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7698910	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs924236	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs924237	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs924238	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs924239	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs924240	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs964693	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs964694	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs964695	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs996281	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs996282	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9997640	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9999649	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878774	chr4:28153349-28254938	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv878776	chr4:28208093-28267024	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	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
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7686001	CCDC149	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:28235000-28279200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:28249600-28250200	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr4:28249800-28250000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:28249800-28250200	Enhancers	Brain Substantia Nigra	brain

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