Variant report

Variant	rs1518522
Chromosome Location	chr11:18037644-18037645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18036213..18038054-chr11:18118246..18120571,2	MCF-7	breast:
2	chr11:18037112..18038638-chr11:18097036..18099168,2	K562	blood:
3	chr11:18034918..18037858-chr11:18041029..18043888,2	K562	blood:
4	chr11:18033853..18039770-chr11:18040771..18045725,5	K562	blood:
5	chr11:18025939..18028718-chr11:18036280..18038941,2	K562	blood:

Variant related genes	Relation type
ENSG00000129167	Chromatin interaction
ENSG00000129158	Chromatin interaction
ENSG00000255448	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10741734	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10766446	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10832872	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832874	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11024446	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12292490	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1401163	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1401164	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1518521	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1607395	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs169806	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1799913	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1800532	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs188397	0.82[EUR][1000 genomes]
rs2041244	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2056246	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2071532	0.89[EUR][1000 genomes]
rs211095	0.81[EUR][1000 genomes]
rs211096	0.81[EUR][1000 genomes]
rs211097	0.82[EUR][1000 genomes]
rs211098	0.82[EUR][1000 genomes]
rs211106	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs211107	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs211108	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs211140	0.83[EUR][1000 genomes]
rs211141	0.83[EUR][1000 genomes]
rs211144	0.83[EUR][1000 genomes]
rs211148	0.80[EUR][1000 genomes]
rs211149	0.81[EUR][1000 genomes]
rs211150	0.81[EUR][1000 genomes]
rs211151	0.81[EUR][1000 genomes]
rs2237907	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2237908	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2237909	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2237911	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2283233	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2283235	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2299625	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2670764	0.81[EUR][1000 genomes]
rs2670765	0.81[EUR][1000 genomes]
rs508924	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs517005	0.86[EUR][1000 genomes]
rs544437	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs546383	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs572940	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs593839	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs616099	0.81[EUR][1000 genomes]
rs652458	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs654734	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs684302	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs685249	0.81[AMR][1000 genomes]
rs685657	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72862028	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7927135	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7933505	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs887242	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9787863	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv897026	chr11:17823296-18084878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv832079	chr11:17927967-18047743	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1518522	SERGEF	cis	Muscle Skeletal	GTEx
rs1518522	SERGEF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18035600-18038400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:18035600-18048600	Weak transcription	Ovary	ovary
3	chr11:18036000-18040000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr11:18036000-18046000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:18036400-18041000	Weak transcription	Aorta	Aorta
6	chr11:18036800-18045400	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links