Variant report

Variant	rs11111949
Chromosome Location	chr12:104641985-104641986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104640550..104643138-chr12:104680715..104683734,3	MCF-7	breast:
2	chr12:104637030..104638778-chr12:104641326..104643343,3	K562	blood:
3	chr12:104529888..104531745-chr12:104641591..104644080,2	MCF-7	breast:
4	chr12:104639901..104642308-chr12:104681072..104683014,3	K562	blood:
5	chr12:104641780..104644542-chr12:104647021..104649592,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10861174	0.82[ASN][1000 genomes]
rs10861191	1.00[MEX][hapmap]
rs11111947	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11111948	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11111988	1.00[MEX][hapmap]
rs11832165	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11832923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833441	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11838096	0.88[ASN][1000 genomes]
rs11838099	0.88[ASN][1000 genomes]
rs12299988	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12302458	1.00[MEX][hapmap]
rs12312443	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035284	0.88[ASN][1000 genomes]
rs17806577	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs28651552	0.94[ASN][1000 genomes]
rs34217906	0.89[ASN][1000 genomes]
rs34494070	0.89[ASN][1000 genomes]
rs35009941	1.00[EUR][1000 genomes]
rs35456434	1.00[EUR][1000 genomes]
rs35531900	1.00[EUR][1000 genomes]
rs41453549	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4576900	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap]
rs56406045	0.94[ASN][1000 genomes]
rs57036458	0.88[ASN][1000 genomes]
rs58420147	0.88[ASN][1000 genomes]
rs59097029	0.82[ASN][1000 genomes]
rs59259947	1.00[ASN][1000 genomes]
rs60333117	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61109788	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61116111	0.88[ASN][1000 genomes]
rs61234792	0.82[ASN][1000 genomes]
rs61485460	0.88[ASN][1000 genomes]
rs61497238	0.88[ASN][1000 genomes]
rs61665972	0.88[ASN][1000 genomes]
rs7303284	1.00[CHB][hapmap]
rs7313573	0.82[ASN][1000 genomes]
rs7958103	1.00[CHB][hapmap]
rs7979713	1.00[CHB][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	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
2	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
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11111949	PRRX1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104638000-104642400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr12:104638000-104642400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr12:104641000-104642600	Enhancers	A549	lung
4	chr12:104641400-104642000	Enhancers	Hela-S3	cervix
5	chr12:104641600-104643000	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr12:104641600-104643000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:104641600-104643000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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