Variant report

Variant	rs41324645
Chromosome Location	chr8:39809352-39809353
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10089533	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10099498	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10104314	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10216703	0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10958575	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11783682	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2001211	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2007028	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2052378	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2340951	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2543043	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2543045	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2543048	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2543052	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2543083	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2543084	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2543085	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2729457	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729461	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729463	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729486	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729487	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729489	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729491	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28666749	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66694577	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6983467	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6990252	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7008770	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72643908	0.89[AFR][1000 genomes]
rs7820690	0.96[EUR][1000 genomes];0.91[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	nsv539555	chr8:39683857-40673606	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1033371	chr8:39749437-39899540	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs41324645	PLEKHA2	cis	cerebellum	SCAN
rs41324645	CHRNB3	cis	cerebellum	SCAN
rs41324645	TM2D2	cis	Muscle Skeletal	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:39805000-39809800	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr8:39805400-39810200	Enhancers	Primary hematopoietic stem cells	blood
3	chr8:39806000-39817000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr8:39806200-39810000	Active TSS	Liver	Liver
5	chr8:39807000-39809400	Weak transcription	A549	lung
6	chr8:39807600-39809600	Enhancers	Primary B cells from cord blood	blood
7	chr8:39808200-39809800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
8	chr8:39808400-39809400	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr8:39808600-39809600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr8:39808800-39809400	Flanking Active TSS	K562	blood
11	chr8:39808800-39810400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr8:39809000-39809400	Weak transcription	Left Ventricle	heart
13	chr8:39809000-39809800	Active TSS	Duodenum Mucosa	Duodenum
14	chr8:39809000-39810200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr8:39809000-39810200	Flanking Active TSS	GM12878-XiMat	blood
16	chr8:39809000-39810400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr8:39809200-39809600	Active TSS	Placenta	Placenta
18	chr8:39809200-39809800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr8:39809200-39810000	Flanking Active TSS	Primary B cells from peripheral blood	blood
20	chr8:39809200-39810000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr8:39809200-39810000	Active TSS	Adipose Nuclei	Adipose
22	chr8:39809200-39810200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

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