Variant report

Variant	rs6539125
Chromosome Location	chr12:104561521-104561522
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	JUND	chr12:104561165-104561853	T-47D	breast:	n/a	n/a
2	NR3C1	chr12:104561240-104561599	A549	lung:	n/a	chr12:104561425-104561439 chr12:104561423-104561440
3	EP300	chr12:104561191-104561632	T-47D	breast:	n/a	n/a
4	RCOR1	chr12:104561438-104561698	K562	blood:	n/a	n/a
5	GATA3	chr12:104561294-104561632	T-47D	breast:	n/a	chr12:104561570-104561579 chr12:104561386-104561396 chr12:104561567-104561583 chr12:104561565-104561586
6	NR3C1	chr12:104561288-104561552	A549	lung:	n/a	chr12:104561425-104561439 chr12:104561423-104561440
7	NR3C1	chr12:104561333-104561653	A549	lung:	n/a	chr12:104561425-104561439 chr12:104561423-104561440

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104556259..104558196-chr12:104560422..104562244,2	K562	blood:
2	chr12:104560247..104562977-chr12:104565263..104567117,2	K562	blood:

Variant related genes	Relation type
ENSG00000257193	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11111913	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11111916	0.82[JPT][hapmap]
rs11111917	0.82[JPT][hapmap]
rs11111921	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11111938	1.00[CEU][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11111945	1.00[CEU][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs11536084	0.83[EUR][1000 genomes]
rs11836726	0.82[JPT][hapmap]
rs2629745	0.83[CEU][hapmap]
rs2629755	0.93[MEX][hapmap]
rs4246260	0.82[JPT][hapmap]
rs4628754	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4964628	0.82[JPT][hapmap]
rs4964635	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7310815	1.00[CEU][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7311546	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7312300	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7487242	0.83[EUR][1000 genomes]
rs7954970	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7957744	0.82[JPT][hapmap]
rs7966740	0.84[ASN][1000 genomes]
rs7972172	0.82[JPT][hapmap]

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	nsv1045725	chr12:104524153-104614108	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
2	nsv541586	chr12:104524153-104614108	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
3	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
4	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6539125	PMCH	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104559200-104563800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:104560000-104562800	Enhancers	Placenta	Placenta
3	chr12:104560600-104563800	Weak transcription	Right Ventricle	heart
4	chr12:104560600-104565800	Weak transcription	Spleen	Spleen

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