Variant report

Variant	rs66512005
Chromosome Location	chr5:1973758-1973759
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:1964453..1969869-chr5:1973026..1976293,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249731	Chromatin interaction
ENSG00000248597	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10037957	0.92[ASN][1000 genomes]
rs10038712	0.92[ASN][1000 genomes]
rs10040620	0.92[ASN][1000 genomes]
rs10076791	0.85[ASN][1000 genomes]
rs10512638	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11133919	0.83[ASN][1000 genomes]
rs12513689	0.95[ASN][1000 genomes]
rs12659582	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13179979	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13187786	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16902181	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2087141	0.92[ASN][1000 genomes]
rs33941693	0.92[ASN][1000 genomes]
rs34262770	0.92[ASN][1000 genomes]
rs35479209	0.92[ASN][1000 genomes]
rs4277952	0.86[ASN][1000 genomes]
rs4493711	0.86[ASN][1000 genomes]
rs4583926	0.86[ASN][1000 genomes]
rs4975778	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975781	0.90[ASN][1000 genomes]
rs4975785	0.86[ASN][1000 genomes]
rs56350722	0.92[ASN][1000 genomes]
rs62337136	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62337140	0.92[ASN][1000 genomes]
rs72708618	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs746364	0.86[ASN][1000 genomes]
rs746365	0.86[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	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv508344	chr5:1905222-1976860	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv881562	chr5:1907974-1976187	Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv427705	chr5:1950467-2115059	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv4681	chr5:1967628-2010091	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1967000-1973800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:1971600-1973800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr5:1972800-1973800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:1973400-1973800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:1973400-1974200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:1973400-1974400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr5:1973400-1974400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
8	chr5:1973400-1975800	Flanking Active TSS	HMEC	breast
9	chr5:1973600-1973800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
10	chr5:1973600-1973800	Enhancers	Esophagus	oesophagus
11	chr5:1973600-1974000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr5:1973600-1974000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:1973600-1974000	Bivalent Enhancer	Brain Cingulate Gyrus	brain
14	chr5:1973600-1974000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
15	chr5:1973600-1974000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
16	chr5:1973600-1974200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:1973600-1974200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr5:1973600-1974200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
19	chr5:1973600-1975600	Flanking Active TSS	NHEK	skin

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