Variant report

Variant	rs7254809
Chromosome Location	chr19:38365695-38365696
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	chr19:38359287..38362108-chr19:38365312..38367843,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1056405	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11083434	0.98[EUR][1000 genomes]
rs11083442	0.81[EUR][1000 genomes]
rs11665869	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666021	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11667246	0.80[AMR][1000 genomes]
rs11668748	0.81[EUR][1000 genomes]
rs11672257	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11672440	1.00[CEU][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs11672673	0.81[EUR][1000 genomes]
rs11672724	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs12460735	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17249047	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2382624	0.82[EUR][1000 genomes]
rs241935	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs241952	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs241954	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs241955	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs35205379	0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap]
rs3848624	0.91[EUR][1000 genomes]
rs4088299	0.93[EUR][1000 genomes]
rs4356596	0.93[EUR][1000 genomes]
rs4510143	0.93[EUR][1000 genomes]
rs56672492	0.81[AMR][1000 genomes]
rs60731897	0.92[EUR][1000 genomes]
rs73025630	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73027418	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73029180	0.82[EUR][1000 genomes]
rs73041004	0.91[EUR][1000 genomes]
rs73041022	0.93[EUR][1000 genomes]
rs73041034	0.98[EUR][1000 genomes]
rs73041045	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73041047	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8103383	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1062040	chr19:38294465-38370456	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1825275	chr19:38341754-38376485	Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv960836	chr19:38355208-38370306	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7254809	MRPS12	cis	cerebellum	SCAN
rs7254809	PLEKHG2	cis	cerebellum	SCAN
rs7254809	FOSB	cis	cerebellum	SCAN
rs7254809	PSMC4	cis	parietal	SCAN
rs7254809	CEACAM3	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38365400-38365800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr19:38365400-38366200	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr19:38365400-38366200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr19:38365400-38367400	Enhancers	HepG2	liver
5	chr19:38365600-38365800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:38365600-38366000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr19:38365600-38366000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr19:38365600-38366000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr19:38365600-38366200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
10	chr19:38365600-38366200	Enhancers	H9 Cell Line	embryonic stem cell
11	chr19:38365600-38366200	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr19:38365600-38367000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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