Variant report

Variant	rs4975943
Chromosome Location	chr3:51862453-51862454
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51862209..51864973-chr3:51975409..51978321,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114767	Chromatin interaction
ENSG00000041880	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10035839	0.86[AFR][1000 genomes]
rs10053628	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10054179	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10054540	0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10055898	0.85[AFR][1000 genomes]
rs10058065	0.86[AFR][1000 genomes]
rs10059207	0.81[AFR][1000 genomes]
rs10060408	0.82[AFR][1000 genomes]
rs10062139	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10065204	0.84[ASN][1000 genomes]
rs10071996	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10080117	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10213721	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10214016	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10214118	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10214255	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10214256	0.93[ASN][1000 genomes]
rs10462113	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10473426	0.82[AFR][1000 genomes]
rs10941803	0.83[AFR][1000 genomes]
rs10941822	0.84[ASN][1000 genomes]
rs10941823	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11744550	0.81[AFR][1000 genomes]
rs11748472	0.92[AFR][1000 genomes]
rs12513540	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12518422	0.86[EUR][1000 genomes]
rs12518698	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12522625	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12657568	0.92[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs13157277	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13187523	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13187720	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13354339	0.82[AFR][1000 genomes]
rs13358908	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs28816502	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28847123	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28855077	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34101830	0.81[AFR][1000 genomes]
rs34647604	0.81[AFR][1000 genomes]
rs36019653	0.82[AFR][1000 genomes]
rs36031455	0.89[AFR][1000 genomes]
rs4975899	0.84[AFR][1000 genomes]
rs4975901	0.81[AFR][1000 genomes]
rs4975904	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4975927	0.86[AFR][1000 genomes]
rs4975938	0.86[AFR][1000 genomes]
rs4975940	0.94[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4975941	0.93[ASN][1000 genomes]
rs4975942	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975944	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4975950	0.86[AFR][1000 genomes]
rs61351693	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7293325	0.85[ASN][1000 genomes]
rs7293371	0.84[AFR][1000 genomes]
rs7293440	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7293442	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7293446	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs8175436	0.80[ASN][1000 genomes]
rs8185006	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs8185011	0.91[AFR][1000 genomes]
rs8185088	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8185220	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8185247	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs8185248	0.81[AFR][1000 genomes]
rs8185288	0.87[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs8185303	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs8185329	0.88[AFR][1000 genomes]
rs8185354	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs8185356	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs8188228	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs8188256	0.97[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs8188260	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv3416846	chr3:51781117-51888179	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
6	nsv1001350	chr3:51860817-51899966	Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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