Variant report

Variant	rs7519854
Chromosome Location	chr1:159772560-159772561
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:159767187..159770392-chr1:159770720..159774821,3	K562	blood:

Variant related genes	Relation type
ENSG00000181036	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11265280	0.89[GIH][hapmap]
rs11265282	0.90[TSI][hapmap]
rs11591079	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs2494495	0.88[CEU][hapmap]
rs2501343	0.83[CEU][hapmap]
rs4656246	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55742616	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55997732	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs61821619	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61821621	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61821622	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61821626	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61821627	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61821659	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823160	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823162	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823163	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823164	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823165	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72700609	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72700610	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72700611	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72700615	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72700621	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72700626	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72700627	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72700628	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72700632	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72700634	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7512164	0.89[GIH][hapmap]
rs7525794	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528163	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549918	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv521503	chr1:159762120-159795478	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7519854	COPA	cis	cerebellum	SCAN
rs7519854	FCRL6	cis	multi-tissue	Pritchard
rs7519854	OLFML2B	cis	cerebellum	SCAN
rs7519854	HAPLN2	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159769000-159773200	Weak transcription	Placenta	Placenta
2	chr1:159769800-159774400	Weak transcription	NHDF-Ad	bronchial
3	chr1:159770000-159774000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr1:159770400-159773600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:159770600-159772800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:159770600-159774000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:159771000-159776600	Weak transcription	Primary T cells from cord blood	blood
8	chr1:159771400-159773800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:159771600-159774600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:159771600-159774600	Enhancers	Spleen	Spleen
11	chr1:159771800-159774000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
12	chr1:159772000-159772600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr1:159772200-159772800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:159772200-159773200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
15	chr1:159772200-159773200	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr1:159772400-159773200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:159772400-159773400	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links