Variant report

Variant	rs7314278
Chromosome Location	chr12:124380014-124380015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124379315..124381035-chr12:124454320..124456842,2	MCF-7	breast:
2	chr12:124378198..124380132-chr12:124382297..124384260,2	K562	blood:
3	chr12:124377023..124380041-chr12:124383288..124384987,3	MCF-7	breast:
4	chr12:124379452..124381499-chr12:124383777..124386818,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179195	Chromatin interaction
ENSG00000270095	Chromatin interaction
ENSG00000270061	Chromatin interaction
ENSG00000119242	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10773041	0.89[ASN][1000 genomes]
rs10773046	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[ASN][1000 genomes]
rs10773047	0.97[ASN][1000 genomes]
rs10846562	0.90[JPT][hapmap]
rs10846564	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10846567	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10846570	0.89[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10846571	0.88[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10846572	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10846573	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10846574	0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs10846575	0.84[ASN][1000 genomes]
rs10846576	0.88[ASN][1000 genomes]
rs11057381	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11057383	0.88[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11057388	0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[ASN][1000 genomes]
rs11057389	1.00[ASN][1000 genomes]
rs11057390	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12306328	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[ASN][1000 genomes]
rs12307524	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12309481	0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1317312	0.95[JPT][hapmap]
rs1317386	0.88[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1882489	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1922258	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2341569	0.84[ASN][1000 genomes]
rs2341779	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs28435362	0.88[ASN][1000 genomes]
rs28528904	0.88[ASN][1000 genomes]
rs28654550	0.88[ASN][1000 genomes]
rs34587940	0.87[ASN][1000 genomes]
rs4390427	0.95[ASN][1000 genomes]
rs4930727	0.87[ASN][1000 genomes]
rs57078519	0.88[ASN][1000 genomes]
rs57316347	0.88[ASN][1000 genomes]
rs58411567	0.88[ASN][1000 genomes]
rs61587964	0.88[ASN][1000 genomes]
rs6488907	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6488910	0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7296123	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7297429	0.90[ASN][1000 genomes]
rs7300037	0.88[ASN][1000 genomes]
rs7303634	0.99[ASN][1000 genomes]
rs7313897	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7314335	0.88[ASN][1000 genomes]
rs7959519	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7964324	0.88[ASN][1000 genomes]
rs7970597	0.88[ASN][1000 genomes]
rs7976319	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7977078	0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7977713	0.90[JPT][hapmap]
rs7978781	0.88[ASN][1000 genomes]
rs9669530	0.88[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7314278	PITPNM2	cis	cerebellum	SCAN
rs7314278	RILPL2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124376600-124383200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:124378400-124380600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr12:124379200-124380800	Bivalent Enhancer	HepG2	liver
4	chr12:124379600-124380200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr12:124380000-124380400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:124380000-124385600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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