Variant report

Variant	rs12492699
Chromosome Location	chr3:151011944-151011945
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:151011307..151016157-chr3:151019117..151025599,7	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1125541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11708287	0.89[JPT][hapmap]
rs11715892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11717634	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12487835	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12494865	0.90[CEU][hapmap]
rs13088531	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13090321	0.91[EUR][1000 genomes]
rs1352886	0.84[CEU][hapmap]
rs1388627	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1388628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16863323	0.90[CEU][hapmap]
rs16863334	0.84[CEU][hapmap]
rs16863336	0.84[CEU][hapmap]
rs17204376	1.00[ASW][hapmap]
rs3971192	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4076581	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs41399847	0.82[JPT][hapmap]
rs4679794	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6793061	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.86[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	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12492699	GPR171	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150984400-151022400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:151002000-151012000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:151002400-151018000	Weak transcription	NHLF	lung
4	chr3:151002600-151044000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:151005200-151014000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:151009600-151018200	Strong transcription	HMEC	breast
7	chr3:151009800-151016000	Weak transcription	Aorta	Aorta
8	chr3:151010200-151022200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:151010400-151019000	Strong transcription	NHEK	skin
10	chr3:151010600-151018800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:151010800-151013200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:151010800-151018200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:151011200-151012800	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:151011200-151013400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:151011200-151018800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:151011400-151021800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:151011600-151012200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:151011800-151012400	Weak transcription	Esophagus	oesophagus
19	chr3:151011800-151021600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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