Variant report

Variant	rs2139634
Chromosome Location	chr3:46521392-46521393
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46518251..46521004-chr3:46521282..46522790,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10514713	1.00[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs10865941	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10865942	0.90[JPT][hapmap]
rs11130093	1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs11130094	1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs11706090	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11719033	0.80[EUR][1000 genomes]
rs12489007	0.80[EUR][1000 genomes]
rs12489117	0.83[EUR][1000 genomes]
rs12490169	0.80[EUR][1000 genomes]
rs12496623	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs12638228	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1402151	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs1520483	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17078932	0.83[YRI][hapmap]
rs2280407	0.80[EUR][1000 genomes]
rs28413725	0.80[EUR][1000 genomes]
rs3934896	0.80[EUR][1000 genomes]
rs4683242	0.82[JPT][hapmap]
rs55950019	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56233078	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60986461	0.80[EUR][1000 genomes]
rs6762703	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763280	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883739	1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.80[EUR][1000 genomes]
rs883740	0.82[JPT][hapmap]
rs885485	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs885486	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014624	chr3:46463424-46549188	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1009892	chr3:46496775-46546918	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv536553	chr3:46496775-46546918	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2139634	LRRC2	cis	parietal	SCAN
rs2139634	KIF9	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46507400-46522400	Weak transcription	Gastric	stomach
2	chr3:46511800-46530200	Weak transcription	Right Atrium	heart
3	chr3:46513400-46525800	Weak transcription	Left Ventricle	heart
4	chr3:46520200-46521800	Weak transcription	Fetal Intestine Large	intestine
5	chr3:46520200-46522000	Weak transcription	Fetal Intestine Small	intestine
6	chr3:46520400-46523600	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr3:46520800-46521800	Weak transcription	Spleen	Spleen
8	chr3:46520800-46522400	Weak transcription	Pancreas	Pancrea
9	chr3:46520800-46523000	Enhancers	Brain Hippocampus Middle	brain
10	chr3:46521000-46521800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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