Variant report

Variant	rs12516321
Chromosome Location	chr5:60549110-60549111
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr5:60549012-60549765	SH-SY5Y	brain:	n/a	chr5:60549089-60549096 chr5:60549069-60549086 chr5:60549089-60549096 chr5:60549087-60549097 chr5:60549080-60549087 chr5:60549080-60549087 chr5:60549082-60549103 chr5:60549087-60549096 chr5:60549089-60549096 chr5:60549080-60549087
2	GATA2	chr5:60549102-60549791	SH-SY5Y	brain:	n/a	chr5:60549759-60549769

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60548575..60550984-chr5:60558808..60560811,2	K562	blood:
2	chr5:60456500..60459341-chr5:60546816..60549547,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249279	TF binding region
ENSG00000251279	Chromatin interaction
ENSG00000249279	Chromatin interaction
ENSG00000188725	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10071281	1.00[ASN][1000 genomes]
rs12153228	1.00[ASN][1000 genomes]
rs124899	0.85[GIH][hapmap];1.00[ASN][1000 genomes]
rs12519764	1.00[ASN][1000 genomes]
rs12520484	1.00[ASN][1000 genomes]
rs12521434	0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs13187930	1.00[ASN][1000 genomes]
rs158701	1.00[ASN][1000 genomes]
rs158702	1.00[ASN][1000 genomes]
rs159359	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159361	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159366	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159368	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159372	1.00[ASN][1000 genomes]
rs2059064	1.00[ASN][1000 genomes]
rs2080870	1.00[ASN][1000 genomes]
rs248686	1.00[ASN][1000 genomes]
rs256373	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28634357	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34499965	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34596	1.00[ASN][1000 genomes]
rs34611	1.00[ASN][1000 genomes]
rs34622	1.00[ASN][1000 genomes]
rs34628	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34630	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34632	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34633	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34784445	1.00[ASN][1000 genomes]
rs62367886	1.00[ASN][1000 genomes]
rs62367887	1.00[ASN][1000 genomes]
rs6893752	1.00[ASN][1000 genomes]
rs71630091	1.00[ASN][1000 genomes]
rs7446842	1.00[ASN][1000 genomes]
rs9291706	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12516321	mimitin	cis	multi-tissue	Pritchard
rs12516321	RAB3C	cis	cerebellum	SCAN
rs12516321	ERCC8	cis	multi-tissue	Pritchard

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60541800-60552600	Weak transcription	A549	lung
2	chr5:60546200-60551000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:60546400-60552000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:60547800-60550400	Enhancers	Ovary	ovary
5	chr5:60548400-60549600	Weak transcription	HSMM	muscle
6	chr5:60548600-60549600	Weak transcription	Pancreas	Pancrea
7	chr5:60548800-60549200	Weak transcription	Stomach Mucosa	stomach
8	chr5:60549000-60552400	Weak transcription	Esophagus	oesophagus

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