Variant report

Variant	rs16952589
Chromosome Location	chr16:47174275-47174276
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:47173268..47175899-chr16:48024944..48027276,2	K562	blood:
2	chr16:47009479..47012393-chr16:47173213..47175154,2	K562	blood:
3	chr16:47174005..47175581-chr16:47176201..47178952,2	MCF-7	breast:
4	chr16:47171642..47174584-chr16:47493767..47496687,2	K562	blood:

Variant related genes	Relation type
ENSG00000129636	Chromatin interaction
ENSG00000102893	Chromatin interaction
ENSG00000260281	Chromatin interaction
ENSG00000171208	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1018171	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11859615	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11860257	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11860969	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11862517	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11865790	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13330181	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13330194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13330832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13331418	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13332032	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13332800	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13333003	0.91[AMR][1000 genomes]
rs13334239	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13334981	0.96[EUR][1000 genomes]
rs13335171	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13339357	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13339406	0.82[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1541589	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16945353	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16945354	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16952126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16952129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16952174	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16952501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16952538	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16952886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16953067	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16953992	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16954067	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16955095	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16955781	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16956024	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16956031	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16956083	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16956093	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2062968	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2078256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28450418	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28457669	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28532949	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28577929	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28681341	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28840689	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28898390	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4386162	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56819508	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56830681	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57543382	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57772915	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58251914	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58837077	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59305841	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59453301	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59547333	0.89[EUR][1000 genomes]
rs59992453	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60237214	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61078258	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6598800	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7184206	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7185641	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7186492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7188942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7192537	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7197586	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7197973	0.93[EUR][1000 genomes]
rs7199958	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7200041	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7200149	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7201148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7202716	0.89[EUR][1000 genomes]
rs7202975	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7206669	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73536876	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73536884	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73536895	1.00[EUR][1000 genomes]
rs73536899	1.00[EUR][1000 genomes]
rs73538910	0.93[EUR][1000 genomes]
rs73538974	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73538980	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73538991	0.89[EUR][1000 genomes]
rs73538993	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73538997	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73539001	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73541004	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73541007	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73541010	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73541086	0.89[EUR][1000 genomes]
rs73541089	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73541102	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73543108	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73543111	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73543118	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7498593	0.89[EUR][1000 genomes]
rs7499413	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8044842	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8047754	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8048801	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053323	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8055882	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8063584	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9328707	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9921947	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9922635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923731	1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9926965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9927084	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9928466	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9928688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9935641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9936810	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939920	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	esv1840592	chr16:47171333-47177650	Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	esv1821100	chr16:47171333-47330244	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16952589	Hs.42217	cis	multi-tissue	Pritchard

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:47148000-47175400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr16:47156200-47175800	Weak transcription	Psoas Muscle	Psoas
3	chr16:47157400-47175600	Weak transcription	HSMM	muscle
4	chr16:47161600-47175800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr16:47164000-47175600	Weak transcription	NHLF	lung
6	chr16:47169200-47174600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr16:47170000-47175400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr16:47170400-47175800	Weak transcription	Gastric	stomach
9	chr16:47170600-47175400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr16:47170600-47175600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr16:47171000-47175000	Enhancers	Fetal Brain Male	brain
12	chr16:47171000-47175600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr16:47171400-47175400	Enhancers	Hela-S3	cervix
14	chr16:47171400-47175600	Weak transcription	Brain Angular Gyrus	brain
15	chr16:47171400-47175800	Weak transcription	Left Ventricle	heart
16	chr16:47171400-47175800	Weak transcription	Spleen	Spleen
17	chr16:47171800-47175400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr16:47172000-47175600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr16:47172200-47175400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr16:47172600-47175200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr16:47172600-47175400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr16:47172600-47175400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr16:47172800-47175400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr16:47172800-47175400	Weak transcription	HUVEC	blood vessel
25	chr16:47173000-47174600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr16:47173200-47174600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr16:47173200-47175400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr16:47173200-47175400	Weak transcription	K562	blood
29	chr16:47173400-47175400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr16:47173400-47175600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr16:47173600-47175000	Flanking Active TSS	NHEK	skin
32	chr16:47173800-47175400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr16:47173800-47175400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr16:47174000-47174800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr16:47174000-47175000	Genic enhancers	A549	lung
36	chr16:47174000-47175200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr16:47174000-47175400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr16:47174000-47175600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr16:47174000-47175600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr16:47174000-47175600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr16:47174200-47174600	Weak transcription	Fetal Brain Female	brain
42	chr16:47174200-47174600	Enhancers	HMEC	breast
43	chr16:47174200-47174800	Weak transcription	Brain Germinal Matrix	brain
44	chr16:47174200-47175000	Weak transcription	NH-A	brain
45	chr16:47174200-47175200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr16:47174200-47178400	Active TSS	GM12878-XiMat	blood

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