Variant report

Variant	rs241935
Chromosome Location	chr19:38293963-38293964
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38225257..38227730-chr19:38293878..38296712,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1056405	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11083430	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11083434	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11665869	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11666021	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11666662	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs11666738	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs11672257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11672440	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs11672724	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs12459013	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs12460230	0.90[JPT][hapmap]
rs12460735	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12462505	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs17249047	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2290999	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs241952	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs241954	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs241955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35205379	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap]
rs3848624	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4088299	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4356596	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4510143	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60731897	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7248397	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7254809	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73025630	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73027418	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73041004	0.92[EUR][1000 genomes]
rs73041022	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73041034	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73041045	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73041047	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8103383	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8108245	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1057428	chr19:38282158-38320814	Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs241935	PSMC4	cis	parietal	SCAN
rs241935	KIAA0961	cis	multi-tissue	Pritchard
rs241935	MRPS12	cis	cerebellum	SCAN
rs241935	PLEKHG2	cis	cerebellum	SCAN
rs241935	FOSB	cis	cerebellum	SCAN
rs241935	CEACAM3	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38291600-38296000	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:38291800-38295400	ZNF genes & repeats	Brain Hippocampus Middle	brain
3	chr19:38291800-38295400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:38292800-38295800	ZNF genes & repeats	Liver	Liver
5	chr19:38292800-38295800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
6	chr19:38292800-38297800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr19:38293200-38295800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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