Variant report

Variant	rs12087642
Chromosome Location	chr1:216769382-216769383
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:216765465..216768393-chr1:216768731..216771064,2	MCF-7	breast:
2	chr1:216768575..216772450-chr1:216772804..216775706,3	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10218694	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863256	0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10863258	0.88[ASN][1000 genomes]
rs11117627	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11117628	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12088947	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1414530	0.83[MEX][hapmap]
rs1419242	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1498276	0.83[MEX][hapmap]
rs1833038	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1833040	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1857401	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2377106	0.96[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4846546	0.90[ASN][1000 genomes]
rs6673566	0.83[MEX][hapmap]
rs6701062	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7519402	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7533692	0.96[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7544758	0.83[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7546236	0.86[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap]
rs7553212	0.86[JPT][hapmap]
rs951034	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];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	nsv549199	chr1:216384908-216814702	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1003815	chr1:216504235-216836498	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv535289	chr1:216504235-216836498	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv873178	chr1:216714314-216813244	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12087642	SMYD2	cis	cerebellum	SCAN
rs12087642	DTL	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216721800-216774000	Weak transcription	Placenta	Placenta
2	chr1:216757400-216773600	Weak transcription	Fetal Intestine Small	intestine
3	chr1:216764800-216769400	Weak transcription	Left Ventricle	heart
4	chr1:216764800-216773400	Weak transcription	Brain Substantia Nigra	brain
5	chr1:216767800-216770000	Enhancers	Fetal Heart	heart
6	chr1:216768800-216770200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:216769000-216769800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:216769000-216770000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr1:216769000-216770000	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr1:216769200-216769400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr1:216769200-216769400	Enhancers	Brain Angular Gyrus	brain
12	chr1:216769200-216769800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:216769200-216770000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:216769200-216770000	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr1:216769200-216770000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr1:216769200-216770000	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:216769200-216770200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:216769200-216770200	Active TSS	Fetal Lung	lung
19	chr1:216769200-216770400	Enhancers	HUES64 Cell Line	embryonic stem cell

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