Variant report

Variant	rs16908555
Chromosome Location	chr9:95567526-95567527
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:95567200-95567644	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr9:95567333-95567723	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95563386..95565101-chr9:95567156..95569894,2	MCF-7	breast:

Variant related genes	Relation type
ANKRD19P	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10821001	0.86[EUR][1000 genomes]
rs10821003	0.86[EUR][1000 genomes]
rs10821004	0.88[EUR][1000 genomes]
rs10821005	0.88[EUR][1000 genomes]
rs10821011	0.87[EUR][1000 genomes]
rs10821014	0.88[EUR][1000 genomes]
rs10821017	0.89[ASN][1000 genomes]
rs10992396	0.85[EUR][1000 genomes]
rs10992406	0.83[CEU][hapmap]
rs10992407	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10992408	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs10992409	0.85[EUR][1000 genomes]
rs10992412	0.85[EUR][1000 genomes]
rs10992414	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10992416	0.85[EUR][1000 genomes]
rs10992417	0.85[EUR][1000 genomes]
rs10992420	0.86[EUR][1000 genomes]
rs10992422	0.88[EUR][1000 genomes]
rs10992423	0.86[EUR][1000 genomes]
rs10992437	0.86[EUR][1000 genomes]
rs10992447	0.92[CEU][hapmap]
rs10992448	0.92[CEU][hapmap];0.92[GIH][hapmap];0.88[EUR][1000 genomes]
rs10992453	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs10992460	0.92[CEU][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs10992461	0.92[CEU][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs10992474	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10992476	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11533010	0.88[EUR][1000 genomes]
rs12057034	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12236754	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs12238691	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs12684076	0.84[EUR][1000 genomes]
rs12684587	0.86[EUR][1000 genomes]
rs12685358	0.88[EUR][1000 genomes]
rs12686771	0.92[CEU][hapmap]
rs16908560	0.84[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[GIH][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1853428	1.00[CEU][hapmap];0.80[GIH][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs1853429	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1974004	1.00[CEU][hapmap];0.80[GIH][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs2181584	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2398780	0.91[CEU][hapmap];0.84[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3739605	0.92[CEU][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs4141966	0.88[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56311406	0.89[EUR][1000 genomes]
rs57737182	0.89[EUR][1000 genomes]
rs58952648	0.88[EUR][1000 genomes]
rs60498616	0.88[EUR][1000 genomes]
rs7031163	0.92[CEU][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs753804	0.88[EUR][1000 genomes]
rs754600	0.81[EUR][1000 genomes]
rs7850075	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7855203	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7859967	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7860628	0.89[EUR][1000 genomes]
rs7863741	0.90[EUR][1000 genomes]
rs7869603	0.88[EUR][1000 genomes]
rs7871537	0.84[CEU][hapmap]
rs912261	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430081	chr9:95502571-95568110	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv831654	chr9:95542920-95720961	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	esv3394460	chr9:95565031-95568629	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3435839	chr9:95565031-95568729	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv972420	chr9:95566045-95588965	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16908555	OMD	cis	parietal	SCAN
rs16908555	IARS	cis	lymphoblastoid	seeQTL
rs16908555	ANKRD19	cis	cerebellum	SCAN
rs16908555	FBP1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95558600-95569600	Weak transcription	Right Atrium	heart
2	chr9:95566600-95569600	Weak transcription	Pancreas	Pancrea
3	chr9:95567000-95567600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links