Variant report

Variant	rs2946788
Chromosome Location	chr11:24010530-24010531
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10767148	0.84[ASN][1000 genomes]
rs10767149	0.84[ASN][1000 genomes]
rs10767150	0.87[ASN][1000 genomes]
rs10834252	0.84[ASN][1000 genomes]
rs10834253	0.80[ASN][1000 genomes]
rs10834258	0.80[ASN][1000 genomes]
rs11027645	0.84[ASN][1000 genomes]
rs11027646	0.84[ASN][1000 genomes]
rs11027647	0.84[ASN][1000 genomes]
rs1915054	0.88[ASN][1000 genomes]
rs1915065	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1915066	0.90[ASN][1000 genomes]
rs1949541	0.80[ASN][1000 genomes]
rs2946787	0.97[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4145287	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4307719	0.81[ASN][1000 genomes]
rs6484002	0.80[ASN][1000 genomes]
rs7118930	0.81[ASN][1000 genomes]
rs7119515	0.83[ASN][1000 genomes]
rs72636024	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897062	chr11:23687928-24031627	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916840	chr11:23710275-24064119	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv897070	chr11:23982573-24074207	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv897071	chr11:23982573-24157765	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv897072	chr11:23995576-24085740	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv467744	chr11:24001975-24061085	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv553772	chr11:24001975-24061085	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv467745	chr11:24001975-24091682	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv553773	chr11:24001975-24091682	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv467746	chr11:24001975-24109916	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv553774	chr11:24001975-24109916	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv553775	chr11:24001975-24323572	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv467747	chr11:24010530-24085740	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv553776	chr11:24010530-24085740	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2946788	LGR4	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:23999200-24012400	Weak transcription	NHLF	lung
2	chr11:24009600-24010600	Active TSS	A549	lung
3	chr11:24009600-24010800	Enhancers	Muscle Satellite Cultured Cells	--
4	chr11:24009600-24011400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:24009800-24010800	Enhancers	HUVEC	blood vessel
6	chr11:24010000-24010600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr11:24010000-24010800	Weak transcription	Osteobl	bone
8	chr11:24010200-24010600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:24010200-24012000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:24010400-24013000	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links