Variant report

Variant	rs12439200
Chromosome Location	chr15:73086731-73086732
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:73075105..73076707-chr15:73086411..73087982,2	K562	blood:
2	chr15:73085797..73088021-chr15:73353697..73355855,2	MCF-7	breast:
3	chr15:73078686..73082116-chr15:73085791..73087796,3	K562	blood:

Variant related genes	Relation type
ENSG00000159322	Chromatin interaction
ENSG00000260898	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11072380	0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs11072383	0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11072389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856110	0.88[ASN][1000 genomes]
rs12437473	1.00[ASN][1000 genomes]
rs12438864	0.90[EUR][1000 genomes]
rs12439473	1.00[ASN][1000 genomes]
rs12591690	0.98[ASN][1000 genomes]
rs12594320	0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12898814	0.86[CHD][hapmap]
rs12902361	0.91[ASN][1000 genomes]
rs12906007	0.93[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12916236	0.99[ASN][1000 genomes]
rs12916448	0.87[ASN][1000 genomes]
rs1346165	0.92[CHB][hapmap];0.96[CHD][hapmap];0.86[ASN][1000 genomes]
rs16957257	0.91[ASN][1000 genomes]
rs16957297	0.93[CHB][hapmap];0.96[CHD][hapmap];0.88[ASN][1000 genomes]
rs2304598	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs28562097	0.96[ASN][1000 genomes]
rs28648660	1.00[ASN][1000 genomes]
rs28737436	1.00[ASN][1000 genomes]
rs28801790	0.99[ASN][1000 genomes]
rs28827493	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28866048	0.88[ASN][1000 genomes]
rs34660767	0.99[ASN][1000 genomes]
rs4777541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495017	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495018	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs7162166	0.86[CHB][hapmap]
rs7170394	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7172397	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7175918	0.91[ASN][1000 genomes]
rs7182854	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs8023358	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs8024644	0.94[ASN][1000 genomes]
rs8026559	0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.88[ASN][1000 genomes]
rs8031691	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs8036269	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758386	chr15:72819785-73120560	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv2760039	chr15:72819785-73120560	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv428307	chr15:72819785-73120560	Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv482512	chr15:73023099-73175952	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12439200	HIGD2B	cis	cerebellum	SCAN
rs12439200	PKM2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73077000-73088800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:73080000-73088800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:73081200-73088800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr15:73082200-73088800	Weak transcription	Ovary	ovary
5	chr15:73083400-73089000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:73083600-73088200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:73083600-73088800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:73086000-73087200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:73086200-73088200	Enhancers	Fetal Stomach	stomach
10	chr15:73086600-73086800	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr15:73086600-73086800	Enhancers	Right Atrium	heart
12	chr15:73086600-73087400	Enhancers	Fetal Lung	lung
13	chr15:73086600-73088800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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