Variant report

Variant	rs17325209
Chromosome Location	chr2:48479210-48479211
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10195717	0.88[CEU][hapmap]
rs10495950	0.92[EUR][1000 genomes]
rs11674317	0.85[EUR][1000 genomes]
rs11674475	0.90[EUR][1000 genomes]
rs11676381	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11676925	0.89[EUR][1000 genomes]
rs11677205	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs11679518	0.84[EUR][1000 genomes]
rs11679956	0.90[EUR][1000 genomes]
rs11680162	0.90[EUR][1000 genomes]
rs11680657	0.99[EUR][1000 genomes]
rs11680968	0.85[EUR][1000 genomes]
rs11681876	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11683689	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11687276	0.85[EUR][1000 genomes]
rs11687401	0.82[EUR][1000 genomes]
rs11687461	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs11687670	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11687851	0.81[EUR][1000 genomes]
rs11687989	0.80[EUR][1000 genomes]
rs11689736	0.90[EUR][1000 genomes]
rs11689818	0.80[EUR][1000 genomes]
rs11691493	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11693267	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11695923	0.99[EUR][1000 genomes]
rs11889493	0.91[EUR][1000 genomes]
rs13398456	0.89[CEU][hapmap]
rs13431982	0.92[EUR][1000 genomes]
rs17324965	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17325048	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17396793	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs17397094	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17397449	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs2014675	0.99[EUR][1000 genomes]
rs2840147	0.84[EUR][1000 genomes]
rs34135365	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4530419	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs55802119	0.92[EUR][1000 genomes]
rs58032869	0.84[EUR][1000 genomes]
rs58136909	0.83[EUR][1000 genomes]
rs6730166	0.92[EUR][1000 genomes]
rs6733558	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs6747738	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6759056	0.90[EUR][1000 genomes]
rs7561696	0.80[EUR][1000 genomes]
rs7571905	0.89[EUR][1000 genomes]
rs7581510	0.92[EUR][1000 genomes]
rs7583719	0.90[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs952468	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1005241	chr2:48413134-48493182	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2762552	chr2:48413146-48493182	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv457407	chr2:48414735-48493182	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv581774	chr2:48414735-48493182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1001850	chr2:48421389-48492090	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv535681	chr2:48421389-48492090	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17325209	KLRAQ1	cis	parietal	SCAN
rs17325209	MSH6	cis	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48475400-48487200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:48476200-48482000	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr2:48476400-48480000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:48476400-48481600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:48477400-48479400	Enhancers	Primary B cells from cord blood	blood
6	chr2:48478000-48479400	Weak transcription	Psoas Muscle	Psoas
7	chr2:48478200-48479400	Enhancers	Liver	Liver
8	chr2:48478200-48480000	Enhancers	HepG2	liver
9	chr2:48478400-48479400	Enhancers	Fetal Intestine Small	intestine
10	chr2:48478600-48479400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr2:48478600-48479400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr2:48479000-48479600	Enhancers	Primary hematopoietic stem cells	blood
13	chr2:48479000-48480200	Weak transcription	GM12878-XiMat	blood
14	chr2:48479000-48481000	Enhancers	K562	blood

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