Variant report

Variant	rs16952538
Chromosome Location	chr16:47168793-47168794
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	chr16:47167732..47169803-chr16:47176534..47179100,2	MCF-7	breast:
2	chr16:47079162..47080799-chr16:47167858..47170799,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171208	Chromatin interaction
ENSG00000260281	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1018171	0.89[EUR][1000 genomes]
rs11859615	1.00[EUR][1000 genomes]
rs11860257	0.89[EUR][1000 genomes]
rs11860969	1.00[EUR][1000 genomes]
rs11862517	0.89[EUR][1000 genomes]
rs11865790	0.86[EUR][1000 genomes]
rs13330181	0.89[EUR][1000 genomes]
rs13330194	0.96[EUR][1000 genomes]
rs13330832	0.89[EUR][1000 genomes]
rs13331418	0.89[EUR][1000 genomes]
rs13332032	0.89[EUR][1000 genomes]
rs13332800	0.93[EUR][1000 genomes]
rs13334239	0.89[EUR][1000 genomes]
rs13334981	0.96[EUR][1000 genomes]
rs13335171	0.89[EUR][1000 genomes]
rs13339357	0.89[EUR][1000 genomes]
rs13339406	0.89[EUR][1000 genomes]
rs1541589	0.89[EUR][1000 genomes]
rs16945353	0.89[EUR][1000 genomes]
rs16952126	1.00[EUR][1000 genomes]
rs16952129	1.00[EUR][1000 genomes]
rs16952174	1.00[EUR][1000 genomes]
rs16952501	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16952589	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16952886	1.00[EUR][1000 genomes]
rs16953067	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16953992	0.89[EUR][1000 genomes]
rs16954067	0.93[EUR][1000 genomes]
rs16955095	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16955781	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16956024	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16956031	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16956083	0.89[EUR][1000 genomes]
rs16956093	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2062968	0.89[EUR][1000 genomes]
rs2078256	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2231981	1.00[EUR][1000 genomes]
rs28450418	0.89[EUR][1000 genomes]
rs28457669	1.00[EUR][1000 genomes]
rs28532949	0.85[EUR][1000 genomes]
rs28577929	0.89[EUR][1000 genomes]
rs28681341	0.89[EUR][1000 genomes]
rs28840689	0.93[EUR][1000 genomes]
rs28898390	0.89[EUR][1000 genomes]
rs4386162	1.00[EUR][1000 genomes]
rs56819508	0.89[EUR][1000 genomes]
rs56830681	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57543382	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57772915	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58251914	0.89[EUR][1000 genomes]
rs58837077	0.89[EUR][1000 genomes]
rs59305841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59453301	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59547333	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59992453	0.93[EUR][1000 genomes]
rs60237214	1.00[EUR][1000 genomes]
rs61078258	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6598800	1.00[EUR][1000 genomes]
rs7184206	1.00[EUR][1000 genomes]
rs7185641	0.89[EUR][1000 genomes]
rs7186492	1.00[EUR][1000 genomes]
rs7188942	1.00[EUR][1000 genomes]
rs7192537	0.89[EUR][1000 genomes]
rs7197586	0.89[EUR][1000 genomes]
rs7197973	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7199958	0.89[EUR][1000 genomes]
rs7200041	0.89[EUR][1000 genomes]
rs7200149	0.89[EUR][1000 genomes]
rs7201148	1.00[EUR][1000 genomes]
rs7202716	0.89[EUR][1000 genomes]
rs7202975	1.00[EUR][1000 genomes]
rs7206669	0.90[EUR][1000 genomes]
rs73536876	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73536884	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73536895	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73536899	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73538910	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73538974	0.89[EUR][1000 genomes]
rs73538980	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73538991	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73538993	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73538997	0.89[EUR][1000 genomes]
rs73539001	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73541004	0.89[EUR][1000 genomes]
rs73541007	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73541010	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73541086	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73541089	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73541102	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73543108	0.89[EUR][1000 genomes]
rs73543111	0.89[EUR][1000 genomes]
rs73543118	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7498593	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7499413	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8044842	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8047754	0.89[EUR][1000 genomes]
rs8048801	1.00[EUR][1000 genomes]
rs8053323	0.89[EUR][1000 genomes]
rs8055882	0.89[EUR][1000 genomes]
rs8063584	0.93[EUR][1000 genomes]
rs9328707	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9921947	0.93[EUR][1000 genomes]
rs9922635	1.00[EUR][1000 genomes]
rs9923731	1.00[EUR][1000 genomes]
rs9926965	1.00[EUR][1000 genomes]
rs9927084	0.86[EUR][1000 genomes]
rs9928466	0.96[EUR][1000 genomes]
rs9928688	1.00[EUR][1000 genomes]
rs9935641	1.00[EUR][1000 genomes]
rs9936810	1.00[EUR][1000 genomes]
rs9939920	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1056328	chr16:47011193-47172862	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	esv1798659	chr16:47083332-47234379	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	esv1823679	chr16:47089357-47194051	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv1795199	chr16:47111119-47732476	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Active 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	28 gene(s)	inside rSNPs	diseases
7	esv1803802	chr16:47115776-47367144	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv906660	chr16:47123724-47347780	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv1059763	chr16:47147194-47373834	ZNF genes & repeats Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv528423	chr16:47163874-47347780	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:47117600-47170200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr16:47143800-47170200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr16:47148000-47175400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr16:47155600-47173000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr16:47156200-47175800	Weak transcription	Psoas Muscle	Psoas
6	chr16:47156800-47170000	Weak transcription	NH-A	brain
7	chr16:47157400-47175600	Weak transcription	HSMM	muscle
8	chr16:47159600-47169000	Weak transcription	HUVEC	blood vessel
9	chr16:47159800-47170600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr16:47161200-47169000	Weak transcription	A549	lung
11	chr16:47161600-47169000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr16:47161600-47175800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr16:47161800-47168800	Weak transcription	Hela-S3	cervix
14	chr16:47161800-47172600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr16:47162400-47170000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr16:47162600-47168800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr16:47162600-47170000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr16:47163000-47169200	Weak transcription	HMEC	breast
19	chr16:47163200-47169200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr16:47163400-47172400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr16:47164000-47175600	Weak transcription	NHLF	lung
22	chr16:47164200-47168800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr16:47164200-47169400	Weak transcription	GM12878-XiMat	blood
24	chr16:47164200-47170000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr16:47164200-47172400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr16:47166200-47169200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr16:47166600-47171200	Weak transcription	K562	blood
28	chr16:47166800-47170000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr16:47168200-47169000	Weak transcription	Fetal Brain Male	brain
30	chr16:47168200-47169400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr16:47168200-47169400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr16:47168200-47171800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr16:47168400-47169200	Weak transcription	NHEK	skin
34	chr16:47168600-47168800	Flanking Active TSS	Fetal Brain Female	brain
35	chr16:47168600-47169000	Flanking Active TSS	Brain Germinal Matrix	brain
36	chr16:47168600-47170000	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr16:47168600-47172600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links