Variant report

Variant	rs12343945
Chromosome Location	chr9:100802907-100802908
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	chr9:100683608..100686455-chr9:100800996..100802948,2	K562	blood:

Variant related genes	Relation type
ENSG00000136932	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10081625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10081626	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10283632	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs10283737	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs10984650	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs10984775	0.88[EUR][1000 genomes]
rs10984811	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs10984822	0.92[EUR][1000 genomes]
rs10984829	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs10984862	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12336903	0.87[EUR][1000 genomes]
rs12338164	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13290142	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28459874	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28549286	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28576751	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28660049	0.88[EUR][1000 genomes]
rs28715400	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66865656	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7030197	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7861102	0.86[EUR][1000 genomes]
rs872251	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][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	nsv482635	chr9:100775549-100953239	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv3493282	chr9:100784615-100805700	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3493283	chr9:100784615-100805700	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12343945	NANS	cis	cerebellum	SCAN
rs12343945	LPPR1	cis	parietal	SCAN
rs12343945	FOXE1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100784000-100803800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:100798000-100807000	Weak transcription	Spleen	Spleen
3	chr9:100798000-100807600	Weak transcription	HSMMtube	muscle
4	chr9:100798200-100807400	Weak transcription	Primary B cells from cord blood	blood
5	chr9:100800200-100807000	Weak transcription	K562	blood
6	chr9:100800400-100806200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:100800600-100805800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr9:100801600-100806000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr9:100801800-100807400	Weak transcription	HSMM	muscle
10	chr9:100802400-100809600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr9:100802800-100803000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr9:100802800-100803800	Enhancers	GM12878-XiMat	blood
13	chr9:100802800-100804800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr9:100802800-100807600	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links