Variant report

Variant	rs4886898
Chromosome Location	chr15:78004743-78004744
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	chr15:78004582..78006437-chr15:78057929..78059969,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11072662	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072663	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072665	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072666	0.81[EUR][1000 genomes]
rs11629729	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11631410	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11633354	0.87[EUR][1000 genomes]
rs11637588	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11856761	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12903563	0.86[EUR][1000 genomes]
rs12911718	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915704	0.83[EUR][1000 genomes]
rs28406214	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34906247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35028279	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35761651	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36058724	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4073356	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4076998	0.89[EUR][1000 genomes]
rs4334265	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4360891	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4477663	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4578613	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4595768	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886521	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886899	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886900	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886902	1.00[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56370262	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495245	0.95[EUR][1000 genomes]
rs7175083	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7176668	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8027520	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8027667	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8043490	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv570141	chr15:77985554-78017361	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv570142	chr15:77993282-78010746	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv570143	chr15:77993282-78017361	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv833061	chr15:77998374-78121905	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv570144	chr15:77999436-78010949	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv570145	chr15:77999436-78012025	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv570146	chr15:78004743-78011408	Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
13	nsv570147	chr15:78004743-78012025	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
14	nsv570148	chr15:78004743-78012504	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
15	nsv570149	chr15:78004743-78012618	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
16	nsv570150	chr15:78004743-78038124	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4886898	CYP1A1	cis	cerebellum	SCAN
rs4886898	SIN3A	cis	parietal	SCAN
rs4886898	NR2E3	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77969200-78007600	Weak transcription	Right Atrium	heart
2	chr15:78002600-78005200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:78003400-78005600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:78003400-78009600	Weak transcription	Brain Germinal Matrix	brain
5	chr15:78003600-78005400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:78003800-78005400	Weak transcription	Fetal Brain Male	brain
7	chr15:78004000-78009800	Weak transcription	Fetal Brain Female	brain
8	chr15:78004200-78005400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:78004200-78006200	Weak transcription	Brain Angular Gyrus	brain
10	chr15:78004400-78005200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr15:78004600-78005400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr15:78004600-78007000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:78004600-78012000	Weak transcription	Brain Inferior Temporal Lobe	brain

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