Variant report

Variant	rs2146719
Chromosome Location	chr9:95558663-95558664
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10117377	0.86[ASN][1000 genomes]
rs10820997	0.87[GIH][hapmap];0.92[MEX][hapmap]
rs10821009	0.80[CEU][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs10821010	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs10821012	0.80[CEU][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs10992413	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs10992418	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10992430	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs10992431	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs10992432	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs10992434	0.80[CEU][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs10992436	0.85[JPT][hapmap]
rs10992442	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs10992443	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs10992444	0.80[CEU][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs10992445	0.80[CEU][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs10992448	0.82[ASW][hapmap]
rs10992451	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs10992460	0.84[ASW][hapmap]
rs10992469	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10992472	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1125063	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs1125064	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs11535540	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12236393	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs12236516	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs12685080	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs12685257	0.80[CEU][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs12685780	0.80[CEU][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs12685791	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs1552908	0.92[MEX][hapmap]
rs1555574	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1810696	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980705	0.92[MEX][hapmap]
rs2181521	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181586	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs2281888	0.92[MEX][hapmap]
rs2296080	0.80[CEU][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs3203916	0.80[CEU][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs556	0.80[CEU][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs753802	0.86[JPT][hapmap]
rs753803	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs7850075	0.82[JPT][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes]
rs7855203	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7862106	0.86[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7863890	0.92[MEX][hapmap]
rs7868651	0.89[ASN][1000 genomes]
rs7871537	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7875225	0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs8181065	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs879812	0.92[MEX][hapmap]
rs976320	0.83[CHB][hapmap];0.84[JPT][hapmap]

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	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	nsv982595	chr9:95551536-95561640	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2146719	BICD2	cis	parietal	SCAN
rs2146719	BICD2	Cis_1M	lymphoblastoid	RTeQTL
rs2146719	ANKRD19	cis	parietal	SCAN
rs2146719	OMD	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95556600-95559000	Enhancers	Fetal Brain Male	brain
2	chr9:95557800-95558800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr9:95558200-95558800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr9:95558400-95559000	Bivalent Enhancer	GM12878-XiMat	blood
5	chr9:95558600-95558800	Flanking Active TSS	HepG2	liver
6	chr9:95558600-95559000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:95558600-95569600	Weak transcription	Right Atrium	heart

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