Variant report

Variant	rs12653245
Chromosome Location	chr5:88693984-88693985
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:88687703..88689475-chr5:88693463..88695074,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10514305	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1158150	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12653011	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12659528	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16867541	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16867551	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16867552	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16867553	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16867554	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16867563	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2059853	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34814331	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56756608	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59842575	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61418152	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6870380	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6876988	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6883052	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6883088	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736534	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];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	nsv532159	chr5:88016214-88783092	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv533373	chr5:88062497-89028098	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv529543	chr5:88348147-88783092	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv830388	chr5:88578939-88793870	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv598927	chr5:88647766-88780868	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
6	nsv830389	chr5:88669984-88860383	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv882357	chr5:88677293-88774328	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
8	nsv882358	chr5:88677293-88776034	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:88692600-88694400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:88692600-88695600	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr5:88692800-88694000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr5:88692800-88695600	Enhancers	Primary B cells from cord blood	blood
5	chr5:88692800-88696000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr5:88693000-88694200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:88693000-88694600	Weak transcription	Primary T cells from cord blood	blood
8	chr5:88693200-88695200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr5:88693200-88695600	Weak transcription	HUVEC	blood vessel
10	chr5:88693600-88694400	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr5:88693600-88694800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr5:88693600-88694800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr5:88693600-88695400	Weak transcription	K562	blood
14	chr5:88693600-88697400	Weak transcription	NHDF-Ad	bronchial
15	chr5:88693800-88694800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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