Variant report

Variant	rs11124590
Chromosome Location	chr2:37777752-37777753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37776380..37779203-chr2:37779985..37783372,3	K562	blood:

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

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

rs_ID	r²[population]
rs10168778	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10173816	0.83[EUR][1000 genomes]
rs10176881	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10181174	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11887848	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11888402	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11895388	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12612951	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12615363	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13002383	0.94[ASN][1000 genomes]
rs13432740	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34369565	0.91[ASN][1000 genomes]
rs34752978	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35422160	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35574342	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35617918	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35745581	0.93[ASN][1000 genomes]
rs35990829	0.91[ASN][1000 genomes]
rs4233923	0.93[ASN][1000 genomes]
rs4404250	0.92[ASN][1000 genomes]
rs4670208	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4670730	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6708088	0.83[EUR][1000 genomes]
rs6710371	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6712065	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67348553	0.91[ASN][1000 genomes]
rs72795708	0.91[ASN][1000 genomes]
rs740992	0.83[EUR][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	nsv833814	chr2:37643132-37840247	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv456374	chr2:37669487-37868214	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv470453	chr2:37669487-37868214	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv581473	chr2:37669487-37868214	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11124590	CDC42EP3	cis	parietal	SCAN
rs11124590	PRKD3	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37771800-37779800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:37774000-37781200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:37774200-37782600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr2:37774800-37778200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr2:37776000-37779200	Weak transcription	HMEC	breast
6	chr2:37776600-37778200	Enhancers	Primary B cells from peripheral blood	blood
7	chr2:37776600-37778200	Flanking Active TSS	GM12878-XiMat	blood
8	chr2:37776600-37778200	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr2:37777000-37777800	Enhancers	Fetal Thymus	thymus
10	chr2:37777200-37777800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:37777400-37777800	Enhancers	Thymus	Thymus
12	chr2:37777400-37778000	Enhancers	Primary B cells from cord blood	blood
13	chr2:37777600-37777800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:37777600-37777800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr2:37777600-37781000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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