Variant report

Variant	rs12306328
Chromosome Location	chr12:124383044-124383045
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:124381734..124384108-chr12:124456893..124459517,2	MCF-7	breast:
2	chr12:124378198..124380132-chr12:124382297..124384260,2	K562	blood:

Variant related genes	Relation type
ENSG00000119242	Chromatin interaction
ENSG00000178882	Chromatin interaction
ENSG00000179195	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10744163	0.91[MKK][hapmap];0.83[YRI][hapmap]
rs10773041	0.89[ASN][1000 genomes]
rs10773046	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10773047	0.97[ASN][1000 genomes]
rs10846562	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs10846564	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10846567	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10846570	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10846571	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10846572	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846574	0.88[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10846575	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10846576	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11057381	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11057383	0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11057388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057389	1.00[ASN][1000 genomes]
rs11057390	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11057391	0.88[EUR][1000 genomes]
rs12307524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309481	0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1317312	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs1317386	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1882489	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1922258	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2341569	0.84[ASN][1000 genomes]
rs2341779	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs28435362	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28528904	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28654550	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34587940	0.82[EUR][1000 genomes];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	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61587964	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6488907	0.89[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	1.00[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	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7314278	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]
rs7314335	0.88[ASN][1000 genomes]
rs7959519	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7964324	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7970597	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7976319	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7977078	0.90[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7977713	0.90[JPT][hapmap]
rs7978781	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9669530	0.94[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12306328	APOL3	trans	cerebellum	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	chr12:124380000-124385600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr12:124381800-124384000	Weak transcription	Fetal Brain Male	brain
4	chr12:124382000-124385400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:124382000-124391400	Weak transcription	Fetal Lung	lung
6	chr12:124382200-124385400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links