Variant report

Variant	rs1414234
Chromosome Location	chr9:21712193-21712194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 127 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10738597	0.81[ASN][1000 genomes]
rs10757236	0.86[ASN][1000 genomes]
rs10757238	0.82[ASN][1000 genomes]
rs10757239	0.82[ASN][1000 genomes]
rs10757240	0.82[ASN][1000 genomes]
rs10757241	0.82[ASN][1000 genomes]
rs10757242	0.81[ASN][1000 genomes]
rs10757245	0.81[ASN][1000 genomes]
rs10757246	0.81[ASN][1000 genomes]
rs10757247	0.81[ASN][1000 genomes]
rs10757251	0.81[ASN][1000 genomes]
rs10811584	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10811592	0.86[ASN][1000 genomes]
rs10811595	0.86[ASN][1000 genomes]
rs10811600	0.82[ASN][1000 genomes]
rs10811601	0.82[ASN][1000 genomes]
rs10811602	0.82[ASN][1000 genomes]
rs10811604	0.81[ASN][1000 genomes]
rs10811605	0.81[ASN][1000 genomes]
rs12380505	0.84[CEU][hapmap];0.83[CHB][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1335498	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1335499	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1335500	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1335501	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1335502	0.82[ASN][1000 genomes]
rs1335505	0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1335506	0.81[ASN][1000 genomes]
rs1335507	0.81[ASN][1000 genomes]
rs1335508	0.81[ASN][1000 genomes]
rs1345027	0.81[ASN][1000 genomes]
rs1372057	0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1372058	0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1372059	0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1414232	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1414233	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1414236	0.81[ASN][1000 genomes]
rs1414237	0.82[ASN][1000 genomes]
rs1414238	0.82[ASN][1000 genomes]
rs1414242	0.89[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1414244	0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1414245	0.81[ASN][1000 genomes]
rs1414246	0.81[ASN][1000 genomes]
rs1414247	0.81[ASN][1000 genomes]
rs1414248	0.81[ASN][1000 genomes]
rs1414249	0.81[ASN][1000 genomes]
rs1452658	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1542075	0.89[CHB][hapmap]
rs1542076	0.89[CHB][hapmap]
rs17833407	0.83[CHB][hapmap]
rs1840050	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1889680	0.88[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1965153	0.83[ASN][1000 genomes]
rs2004627	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2027162	0.81[ASN][1000 genomes]
rs2027163	0.81[ASN][1000 genomes]
rs2043991	0.86[ASN][1000 genomes]
rs2119466	0.81[ASN][1000 genomes]
rs2119467	0.81[ASN][1000 genomes]
rs2123338	0.89[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.84[ASN][1000 genomes]
rs2165408	0.89[CHB][hapmap]
rs2165411	0.86[ASN][1000 genomes]
rs2383202	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2891159	0.89[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2891160	0.82[ASN][1000 genomes]
rs2891164	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2891165	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35875883	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3928894	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs4350062	0.82[ASN][1000 genomes]
rs4352937	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs4364717	0.89[CHB][hapmap]
rs4384075	0.81[ASN][1000 genomes]
rs4548267	0.88[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4560881	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4620363	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4636294	0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs6475549	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6475550	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6475551	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6475552	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6475554	0.86[ASN][1000 genomes]
rs6475555	0.86[ASN][1000 genomes]
rs6475564	0.86[ASN][1000 genomes]
rs6475566	0.82[ASN][1000 genomes]
rs6475568	0.82[ASN][1000 genomes]
rs6475569	0.82[ASN][1000 genomes]
rs6475574	0.81[ASN][1000 genomes]
rs6475585	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7021538	0.82[ASN][1000 genomes]
rs7023299	0.86[ASN][1000 genomes]
rs7023474	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs7028913	0.86[ASN][1000 genomes]
rs7029040	0.86[ASN][1000 genomes]
rs7029166	0.86[ASN][1000 genomes]
rs7029274	0.86[ASN][1000 genomes]
rs7033503	0.83[CHB][hapmap]
rs7039487	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7043827	0.86[ASN][1000 genomes]
rs7047136	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs751173	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7848524	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7852900	0.81[ASN][1000 genomes]
rs7853131	0.81[ASN][1000 genomes]
rs7854018	0.82[ASN][1000 genomes]
rs7854222	0.83[ASN][1000 genomes]
rs7855242	0.86[ASN][1000 genomes]
rs7857636	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7858959	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7858991	0.82[ASN][1000 genomes]
rs7860576	0.86[ASN][1000 genomes]
rs7867994	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7868091	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7871345	0.86[ASN][1000 genomes]
rs7874319	0.82[ASN][1000 genomes]
rs869329	0.83[CHB][hapmap]
rs869330	0.89[CHB][hapmap]
rs871024	0.89[CHB][hapmap]
rs9298821	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9298822	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9298823	0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9298824	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	nsv1029634	chr9:21542970-21765286	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv892743	chr9:21675545-21772064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv471290	chr9:21694038-21721939	Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv892744	chr9:21694039-21746419	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv1837210	chr9:21700795-21729895	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1414234	MTAP	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21707200-21712200	Enhancers	HMEC	breast
2	chr9:21708400-21713000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:21709200-21713000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:21709400-21713400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:21709800-21713000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr9:21710400-21712200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:21710600-21712200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr9:21710600-21712400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:21710800-21712200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr9:21710800-21712400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:21710800-21712600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:21710800-21713000	Enhancers	A549	lung
13	chr9:21711000-21713400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr9:21711200-21712200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr9:21711400-21712600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr9:21711600-21712600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:21711600-21713400	Enhancers	NHEK	skin
18	chr9:21712000-21713000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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