Variant report

Variant	rs55799217
Chromosome Location	chr2:52840203-52840204
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	chr2:52644535..52645157-chr2:52839947..52840842,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11681573	0.85[ASN][1000 genomes]
rs11895971	0.85[ASN][1000 genomes]
rs17043107	0.85[ASN][1000 genomes]
rs1982746	0.86[ASN][1000 genomes]
rs2128961	0.87[ASN][1000 genomes]
rs4672070	0.83[ASN][1000 genomes]
rs4672321	0.85[ASN][1000 genomes]
rs56012334	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56346850	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56384427	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57685027	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59130597	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60581820	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60649086	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62128488	0.86[ASN][1000 genomes]
rs62128489	0.84[ASN][1000 genomes]
rs62128490	0.85[ASN][1000 genomes]
rs6730992	0.87[ASN][1000 genomes]
rs6755042	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6758629	0.94[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7569652	0.82[ASN][1000 genomes]
rs7591634	0.82[ASN][1000 genomes]
rs7596213	0.82[ASN][1000 genomes]
rs7609042	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007633	chr2:52217555-52862389	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv535714	chr2:52217555-52862389	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv874111	chr2:52383698-52962055	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	esv2754871	chr2:52695749-52922949	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv999698	chr2:52720976-52851561	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv834036	chr2:52727240-52916200	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv874125	chr2:52735368-52851073	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv2755042	chr2:52739102-52883790	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1011103	chr2:52754456-52885219	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1004275	chr2:52754716-52885219	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1004695	chr2:52766349-52928948	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv874126	chr2:52783672-52841595	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1011857	chr2:52787949-52945590	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
14	nsv874127	chr2:52797840-52933307	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
15	nsv874128	chr2:52814504-52859829	Enhancers ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv874129	chr2:52826401-52894897	ZNF genes & repeats Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv1013130	chr2:52829113-52893487	Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv1007761	chr2:52829150-52893165	Weak transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv581973	chr2:52829458-52878758	Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv517582	chr2:52829458-52893165	ZNF genes & repeats Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv581974	chr2:52829458-52893165	ZNF genes & repeats Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv874130	chr2:52829458-52894897	ZNF genes & repeats Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	nsv1009555	chr2:52835135-52893487	Enhancers ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:52839000-52840400	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr2:52839400-52844600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:52839800-52840600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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