Variant report

Variant	rs12592547
Chromosome Location	chr15:34411787-34411788
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	chr15:34411334..34412247-chr15:34501831..34502833,4	MCF-7	breast:
2	chr15:34410925..34412547-chr15:34416896..34419566,2	K562	blood:

Variant related genes	Relation type
ENSG00000134152	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11072954	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11634597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11853879	0.85[EUR][1000 genomes]
rs11856158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592403	0.93[ASN][1000 genomes]
rs12592856	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12594048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12903028	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1436923	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs16958770	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1865925	0.91[EUR][1000 genomes]
rs2339374	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568532	0.93[EUR][1000 genomes]
rs2576308	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2576310	0.87[EUR][1000 genomes]
rs28376576	0.95[EUR][1000 genomes]
rs3794593	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4288968	1.00[CEU][hapmap]
rs4468578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4780214	0.93[EUR][1000 genomes]
rs4780215	0.92[EUR][1000 genomes]
rs4780216	1.00[CEU][hapmap];0.83[GIH][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs56310728	0.91[EUR][1000 genomes]
rs6495519	0.93[EUR][1000 genomes]
rs7161835	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7163226	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7182085	0.90[EUR][1000 genomes]
rs721122	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs73374335	0.91[EUR][1000 genomes]
rs8028703	0.91[EUR][1000 genomes]
rs8038259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[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	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers 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	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1035579	chr15:34363159-34501115	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv903986	chr15:34394273-34421951	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12592547	LMOD1	trans	brain	seeQTL
rs12592547	FABP4	trans	brain	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34407600-34413800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:34410000-34411800	Enhancers	Fetal Muscle Leg	muscle
3	chr15:34411400-34411800	Enhancers	A549	lung
4	chr15:34411400-34411800	Enhancers	HSMM	muscle
5	chr15:34411600-34413600	Weak transcription	Placenta	Placenta
6	chr15:34411600-34415000	Weak transcription	HSMMtube	muscle

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