Variant report

Variant	rs2354525
Chromosome Location	chr5:49949720-49949721
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	chr5:49949575..49951807-chr5:49954503..49956971,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10039272	0.87[ASN][1000 genomes]
rs10051561	0.87[ASN][1000 genomes]
rs10058388	0.91[ASN][1000 genomes]
rs10059085	0.87[ASN][1000 genomes]
rs10065432	0.87[ASN][1000 genomes]
rs10072398	0.87[ASN][1000 genomes]
rs12651837	0.80[AFR][1000 genomes]
rs12652605	0.85[EUR][1000 genomes]
rs13356533	0.82[ASN][1000 genomes]
rs13436520	1.00[ASN][1000 genomes]
rs1823263	0.95[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2354526	0.88[ASN][1000 genomes]
rs28495689	0.91[ASN][1000 genomes]
rs28505342	0.87[ASN][1000 genomes]
rs28711235	0.87[ASN][1000 genomes]
rs62366907	0.85[EUR][1000 genomes]
rs6450301	0.88[ASN][1000 genomes]
rs6873522	0.81[AFR][1000 genomes]
rs73097023	0.91[ASN][1000 genomes]
rs7705837	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7728975	0.81[AFR][1000 genomes];0.85[EUR][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	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv16870	chr5:49885849-49989415	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv964851	chr5:49945480-49952101	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2354525	LOC647121	Cis_1M	lymphoblastoid	RTeQTL
rs2354525	PARP8	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49944600-49949800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:49949000-49951200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr5:49949200-49951800	Enhancers	Primary B cells from cord blood	blood
4	chr5:49949400-49950200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr5:49949400-49950200	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr5:49949400-49950200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr5:49949400-49950200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr5:49949400-49950600	Enhancers	GM12878-XiMat	blood
9	chr5:49949400-49951200	Enhancers	Primary B cells from peripheral blood	blood
10	chr5:49949400-49951200	Enhancers	Primary hematopoietic stem cells	blood
11	chr5:49949400-49951600	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr5:49949600-49949800	Enhancers	H9 Cell Line	embryonic stem cell
13	chr5:49949600-49950000	Enhancers	Primary T cells from cord blood	blood
14	chr5:49949600-49950000	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr5:49949600-49950000	Enhancers	Thymus	Thymus
16	chr5:49949600-49950200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr5:49949600-49950200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:49949600-49951000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr5:49949600-49951000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr5:49949600-49952800	Enhancers	Rectal Mucosa Donor 31	rectum

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