Variant report

Variant	rs12915287
Chromosome Location	chr15:50431087-50431088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50343799..50344658-chr15:50430684..50431213,3	MCF-7	breast:
2	chr15:50430804..50433194-chr15:50550057..50552269,2	MCF-7	breast:
3	chr15:50429608..50431277-chr15:50435108..50437577,2	K562	blood:
4	chr15:50408457..50409368-chr15:50430353..50431313,7	MCF-7	breast:
5	chr15:50168681..50169642-chr15:50430274..50431207,4	MCF-7	breast:
6	chr15:50330960..50333313-chr15:50430196..50432185,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104043	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10152738	0.99[ASN][1000 genomes]
rs10519250	1.00[ASW][hapmap]
rs10519262	0.83[ASN][1000 genomes]
rs11070750	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070751	0.81[ASN][1000 genomes]
rs11070752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11070753	0.91[JPT][hapmap];0.80[MKK][hapmap]
rs11631433	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11632133	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11634271	1.00[ASW][hapmap];0.84[GIH][hapmap]
rs11638799	0.81[CEU][hapmap];0.91[YRI][hapmap]
rs11638841	0.81[CEU][hapmap];0.81[YRI][hapmap]
rs12439182	0.81[ASN][1000 genomes]
rs12442998	0.99[ASN][1000 genomes]
rs12443171	0.91[JPT][hapmap];0.91[YRI][hapmap];0.81[ASN][1000 genomes]
rs12591791	0.99[ASN][1000 genomes]
rs12593937	1.00[ASW][hapmap]
rs12901981	0.84[ASN][1000 genomes]
rs12902997	0.99[ASN][1000 genomes]
rs12915042	0.81[CEU][hapmap];0.91[YRI][hapmap]
rs12915230	0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.81[ASN][1000 genomes]
rs12915987	0.91[JPT][hapmap]
rs2413992	1.00[ASW][hapmap]
rs2414025	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs28403229	0.99[ASN][1000 genomes]
rs28650901	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34146758	1.00[ASW][hapmap]
rs4774556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5025069	0.99[ASN][1000 genomes]
rs61214575	0.88[ASN][1000 genomes]
rs7165446	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7171888	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs7177316	0.96[ASN][1000 genomes]
rs7178278	0.96[ASN][1000 genomes]
rs8023371	0.97[ASN][1000 genomes]
rs8027073	1.00[ASW][hapmap]
rs8036777	0.96[ASN][1000 genomes]
rs8037555	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041124	0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs933854	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv569395	chr15:50345393-50437494	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv904208	chr15:50428495-50457858	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12915287	SCG3	cis	parietal	SCAN
rs12915287	ATP8B4	cis	parietal	SCAN
rs12915287	SLC27A2	cis	parietal	SCAN
rs12915287	ATP8B4	cis	brain	BrainEAC
rs12915287	ATP8B4	cis	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50427800-50436400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr15:50428800-50432400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr15:50429000-50434200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr15:50429000-50437000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr15:50429000-50437600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr15:50429600-50434600	Weak transcription	Colon Smooth Muscle	Colon
7	chr15:50429800-50431800	Weak transcription	Fetal Stomach	stomach
8	chr15:50430000-50432200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:50430200-50431200	Enhancers	A549	lung
10	chr15:50430200-50433600	Enhancers	Hela-S3	cervix
11	chr15:50430400-50432600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:50430400-50433000	Weak transcription	HUVEC	blood vessel
13	chr15:50430400-50436800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:50430400-50436800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:50430600-50437000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:50430600-50442600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:50430800-50432000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:50430800-50434400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:50430800-50435400	Weak transcription	NHDF-Ad	bronchial
20	chr15:50430800-50437000	Weak transcription	Osteobl	bone
21	chr15:50431000-50431200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links