Variant report

Variant	rs12309481
Chromosome Location	chr12:124389150-124389151
allele	A/C
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	CTCF	chr12:124389100-124389250	GM12873	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:124387569..124390026-chr12:124455814..124457883,2	MCF-7	breast:
2	chr12:124380887..124382932-chr12:124386966..124389727,2	K562	blood:
3	chr12:124295197..124298095-chr12:124388889..124391568,2	MCF-7	breast:
4	chr12:124369425..124371891-chr12:124388110..124389965,2	MCF-7	breast:

Variant related genes	Relation type
DNAH10	TF binding region
ENSG00000270095	Chromatin interaction
ENSG00000179195	Chromatin interaction
ENSG00000119242	Chromatin interaction
ENSG00000178882	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1054852	0.89[YRI][hapmap]
rs10773046	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10773047	0.86[ASN][1000 genomes]
rs10846562	0.90[JPT][hapmap]
rs10846564	1.00[JPT][hapmap]
rs10846567	1.00[JPT][hapmap]
rs10846570	0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10846571	0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10846572	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10846573	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10846574	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10846575	0.94[ASN][1000 genomes]
rs10846576	0.99[ASN][1000 genomes]
rs11057381	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11057383	0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11057388	0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11057389	0.88[ASN][1000 genomes]
rs11057390	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11057394	0.93[YRI][hapmap]
rs12303671	0.89[YRI][hapmap]
rs12306328	0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12307524	0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12317176	0.93[YRI][hapmap]
rs12809125	0.93[YRI][hapmap]
rs12823740	0.82[YRI][hapmap]
rs1317312	0.95[JPT][hapmap]
rs1317386	0.87[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1882489	1.00[JPT][hapmap]
rs1922258	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2341569	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2341779	1.00[JPT][hapmap]
rs28435362	0.99[ASN][1000 genomes]
rs28528904	0.99[ASN][1000 genomes]
rs28654550	0.99[ASN][1000 genomes]
rs34587940	0.97[ASN][1000 genomes]
rs4390427	0.85[ASN][1000 genomes]
rs57078519	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57316347	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58411567	0.99[ASN][1000 genomes]
rs61587964	0.99[ASN][1000 genomes]
rs6488907	0.95[JPT][hapmap]
rs6488910	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7133378	0.89[YRI][hapmap]
rs7296123	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7297429	0.81[ASN][1000 genomes]
rs7303634	0.88[ASN][1000 genomes]
rs7311969	0.89[YRI][hapmap]
rs7313897	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7314278	0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7959519	1.00[JPT][hapmap]
rs7964324	0.98[ASN][1000 genomes]
rs7970597	0.99[ASN][1000 genomes]
rs7973683	0.89[YRI][hapmap]
rs7976319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977078	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7977713	0.90[JPT][hapmap]
rs7978781	0.99[ASN][1000 genomes]
rs9669530	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs9971695	0.89[YRI][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	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv1811815	chr12:124374716-124424636	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1832870	chr12:124374716-124424636	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv522321	chr12:124383950-124424636	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv560499	chr12:124389150-124396816	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12309481	CCDC92	cis	cerebellum	SCAN
rs12309481	LRRC43	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124382000-124391400	Weak transcription	Fetal Lung	lung
2	chr12:124384000-124408400	Weak transcription	Fetal Brain Female	brain
3	chr12:124385400-124390200	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr12:124386000-124391400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:124386000-124395800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:124386200-124390800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:124386200-124392000	Weak transcription	NH-A	brain
8	chr12:124386200-124392200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:124386200-124394000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:124386800-124391800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:124387200-124392000	Weak transcription	Fetal Thymus	thymus
12	chr12:124388400-124391800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:124388800-124389600	Enhancers	Fetal Kidney	kidney

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