Variant report

Variant	rs2489556
Chromosome Location	chr10:26959202-26959203
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:26958878..26961575-chr10:26966609..26969572,2	K562	blood:
2	chr10:26953025..26955897-chr10:26956336..26959208,3	K562	blood:

Extended variants
information (count: 116 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1008967	0.92[EUR][1000 genomes]
rs10764634	0.82[ASN][1000 genomes]
rs12773328	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1616471	0.82[ASN][1000 genomes]
rs1677715	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1677733	0.89[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1677734	0.82[ASN][1000 genomes]
rs1677735	0.81[ASN][1000 genomes]
rs1677737	0.82[ASN][1000 genomes]
rs1677738	0.88[ASN][1000 genomes]
rs1748340	0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1748341	0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1748342	0.87[ASN][1000 genomes]
rs1748343	0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1748344	0.86[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1748345	0.88[ASN][1000 genomes]
rs1748347	0.89[ASN][1000 genomes]
rs1748348	0.87[ASN][1000 genomes]
rs1748349	0.88[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs1748350	0.80[ASN][1000 genomes]
rs17558625	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17558709	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1780171	0.89[ASN][1000 genomes]
rs1780172	0.88[ASN][1000 genomes]
rs1780173	0.88[ASN][1000 genomes]
rs1812155	0.81[ASN][1000 genomes]
rs1824851	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1830842	0.92[EUR][1000 genomes]
rs1871300	0.83[ASN][1000 genomes]
rs1947788	0.82[ASN][1000 genomes]
rs2005118	0.89[ASN][1000 genomes]
rs2005119	0.98[ASN][1000 genomes]
rs2005253	0.82[ASN][1000 genomes]
rs2011849	0.82[ASN][1000 genomes]
rs2011860	0.82[ASN][1000 genomes]
rs2127142	0.95[EUR][1000 genomes]
rs2224898	0.82[ASN][1000 genomes]
rs2254745	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448089	0.93[EUR][1000 genomes]
rs2448090	0.95[EUR][1000 genomes]
rs2448091	0.92[EUR][1000 genomes]
rs2448092	0.92[EUR][1000 genomes]
rs2448093	0.92[EUR][1000 genomes]
rs2448095	0.93[EUR][1000 genomes]
rs2448108	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2448110	0.99[ASN][1000 genomes]
rs2448113	0.89[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2448114	0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2448116	0.82[ASN][1000 genomes]
rs2448119	0.81[ASN][1000 genomes]
rs2448120	0.82[ASN][1000 genomes]
rs2448128	0.84[ASN][1000 genomes]
rs2448129	0.86[ASN][1000 genomes]
rs2477273	0.93[EUR][1000 genomes]
rs2477274	0.92[EUR][1000 genomes]
rs2477275	0.92[EUR][1000 genomes]
rs2477278	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2477279	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2477280	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2477282	0.99[ASN][1000 genomes]
rs2477283	0.97[ASN][1000 genomes]
rs2477284	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2477288	0.82[ASN][1000 genomes]
rs2477289	0.82[ASN][1000 genomes]
rs2477290	0.82[ASN][1000 genomes]
rs2477291	0.82[ASN][1000 genomes]
rs2477293	0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2489557	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2489560	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2489561	1.00[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs2489565	0.92[EUR][1000 genomes]
rs2489566	0.92[EUR][1000 genomes]
rs2489567	0.92[EUR][1000 genomes]
rs2489568	0.91[EUR][1000 genomes]
rs2489569	0.92[EUR][1000 genomes]
rs2489570	0.92[EUR][1000 genomes]
rs2489584	0.89[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2489586	0.82[ASN][1000 genomes]
rs2489587	0.82[ASN][1000 genomes]
rs2489588	0.82[ASN][1000 genomes]
rs2489590	0.83[ASN][1000 genomes]
rs2489591	0.89[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2489593	0.82[ASN][1000 genomes]
rs2489597	0.81[ASN][1000 genomes]
rs2489600	0.84[ASN][1000 genomes]
rs2489601	0.84[ASN][1000 genomes]
rs2489602	0.99[ASN][1000 genomes]
rs2489603	0.99[ASN][1000 genomes]
rs2887183	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2985470	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2985471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2985487	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2996641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2996642	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2996643	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3118157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118159	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs3118164	0.92[EUR][1000 genomes]
rs7895228	0.82[ASN][1000 genomes]
rs7914153	0.80[ASN][1000 genomes]
rs7919952	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs899374	0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs9334101	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9418574	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv3436664	chr10:26860755-26969397	Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv894977	chr10:26876272-26959202	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1044848	chr10:26890410-26961634	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1052412	chr10:26890945-26961634	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1041766	chr10:26890945-26969381	Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1046911	chr10:26894348-26969381	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1044057	chr10:26894348-26971879	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv516275	chr10:26896432-26968171	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv3333006	chr10:26908323-26985227	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv3353004	chr10:26912762-26966282	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2489556	MTPAP	cis	cerebellum	SCAN
rs2489556	TPRT	cis	multi-tissue	Pritchard
rs2489556	LYZL2	cis	parietal	SCAN
rs2489556	ANKRD26	cis	parietal	SCAN
rs2489556	PDSS1	cis	cerebellum	SCAN
rs2489556	PDSS1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26957000-26962200	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links