Variant report

Variant	rs12363944
Chromosome Location	chr11:76928025-76928026
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	chr11:76919353..76921516-chr11:76926690..76929512,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAK1-5	chr11:76927907-76928359	NONHSAT023209

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11237123	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11237141	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11237142	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11237148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11237150	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11237151	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11237164	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1125619	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12361757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12363707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12363842	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12366261	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12794253	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1670449	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1670450	0.86[AFR][1000 genomes]
rs1670458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes]
rs1670462	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap]
rs17824184	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2156567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes]
rs2725820	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2725822	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3819170	0.87[ASN][1000 genomes]
rs4375461	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs472691	1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap]
rs493256	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap]
rs4945150	1.00[JPT][hapmap]
rs535008	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs558470	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap]
rs561386	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap]
rs563731	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs580624	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs66518011	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66540426	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66728428	0.82[EUR][1000 genomes]
rs686068	1.00[JPT][hapmap]
rs7118943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7934949	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883224	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883680	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897936	chr11:76900813-76935002	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv534515	chr11:76900813-77035769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12363944	PAK1	cis	parietal	SCAN
rs12363944	DNAJB13	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76899800-76928200	Strong transcription	Liver	Liver
2	chr11:76903600-76928600	Strong transcription	Fetal Intestine Small	intestine
3	chr11:76908400-76928200	Strong transcription	Spleen	Spleen
4	chr11:76922600-76930000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:76926000-76939800	Weak transcription	Pancreas	Pancrea
6	chr11:76926400-76934400	Weak transcription	Gastric	stomach
7	chr11:76926600-76937000	Weak transcription	Adipose Nuclei	Adipose
8	chr11:76926600-76937000	Weak transcription	Placenta	Placenta
9	chr11:76927400-76935600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr11:76927400-76936400	Weak transcription	Ovary	ovary
11	chr11:76927800-76934400	Weak transcription	Fetal Intestine Large	intestine

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