Variant report

Variant	rs72940218
Chromosome Location	chr2:110389529-110389530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1046645	0.92[EUR][1000 genomes]
rs10496433	0.81[EUR][1000 genomes]
rs1560884	0.94[EUR][1000 genomes]
rs1836211	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2014730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28464477	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28513618	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28588372	0.83[EUR][1000 genomes]
rs28613553	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28624186	0.80[EUR][1000 genomes]
rs2867277	0.83[EUR][1000 genomes]
rs2867909	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2867910	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28719784	0.93[EUR][1000 genomes]
rs28800201	0.81[EUR][1000 genomes]
rs2903696	0.83[ASN][1000 genomes]
rs2903697	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58360057	0.83[ASN][1000 genomes]
rs59185208	0.83[ASN][1000 genomes]
rs60272411	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61049649	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61428642	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61449947	0.83[ASN][1000 genomes]
rs61548546	0.83[EUR][1000 genomes]
rs6705503	0.98[EUR][1000 genomes]
rs6713646	0.81[EUR][1000 genomes]
rs6760478	0.83[EUR][1000 genomes]
rs726901	0.93[EUR][1000 genomes]
rs72940203	0.81[ASN][1000 genomes]
rs72940214	0.83[ASN][1000 genomes]
rs730988	0.83[ASN][1000 genomes]
rs7568492	0.81[EUR][1000 genomes]
rs7568799	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7572991	0.80[EUR][1000 genomes]
rs7579996	0.94[EUR][1000 genomes]
rs7590230	0.80[EUR][1000 genomes]
rs7603756	0.87[EUR][1000 genomes]
rs9677631	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1009367	chr2:110349178-110863354	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	esv2762780	chr2:110367969-110462496	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv491837	chr2:110381297-110964737	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72940218	SEPT10	cis	Muscle Skeletal	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110387200-110391000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:110387200-110391600	Enhancers	Placenta	Placenta
3	chr2:110387800-110390000	Enhancers	Fetal Intestine Large	intestine
4	chr2:110388200-110389600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:110388200-110389600	Weak transcription	Lung	lung
6	chr2:110388200-110395200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:110388400-110389600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr2:110388400-110389800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:110388400-110395400	Weak transcription	NHEK	skin
10	chr2:110388600-110389600	Weak transcription	Fetal Intestine Small	intestine
11	chr2:110389400-110389800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:110389400-110390200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:110389400-110390200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:110389400-110390200	Enhancers	A549	lung
15	chr2:110389400-110390200	Flanking Active TSS	HepG2	liver
16	chr2:110389400-110391400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr2:110389400-110392200	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links