Variant report

Variant	rs2943693
Chromosome Location	chr12:57835965-57835966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57823739..57827360-chr12:57835949..57840041,5	K562	blood:
2	chr12:57834476..57836916-chr12:57849155..57853126,3	K562	blood:
3	chr12:57824691..57826553-chr12:57834821..57837782,2	MCF-7	breast:
4	chr12:57823623..57830869-chr12:57831560..57839261,11	K562	blood:
5	chr12:57830432..57832842-chr12:57835916..57837461,2	MCF-7	breast:
6	chr12:57822828..57827240-chr12:57828141..57836129,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139269	Chromatin interaction
ENSG00000258001	Chromatin interaction
ENSG00000175189	Chromatin interaction
ENSG00000179912	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10876968	0.83[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap]
rs11172142	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11172155	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs11830804	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap]
rs12227309	0.91[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap]
rs12820078	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2943691	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2943692	1.00[CEU][hapmap];0.80[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3204635	0.82[GIH][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap]
rs473465	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs487722	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs501055	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs505479	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs507562	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs519452	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs538548	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs567895	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs568793	0.84[JPT][hapmap]
rs572198	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7297282	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7302906	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap]
rs7303542	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73115907	0.85[EUR][1000 genomes]
rs9738646	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2943693	KIAA0748	cis	cerebellum	SCAN
rs2943693	DNAJC14	cis	cerebellum	SCAN
rs2943693	SP7	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57825600-57848600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:57829400-57843200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:57833000-57836200	Weak transcription	Aorta	Aorta
4	chr12:57833400-57843600	Weak transcription	HepG2	liver
5	chr12:57835800-57836400	Genic enhancers	Liver	Liver

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