Variant report

Variant	rs9889227
Chromosome Location	chr17:16534851-16534852
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF287-2	chr17:16534658-16535029	NONHSAT145989

Extended variants
information (count: 122 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1005369	1.00[ASN][1000 genomes]
rs1005370	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12051673	0.96[ASN][1000 genomes]
rs12051751	0.88[EUR][1000 genomes]
rs12103873	0.84[ASN][1000 genomes]
rs16959857	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16959869	1.00[ASN][1000 genomes]
rs16959870	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28431824	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28458310	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28458353	0.98[ASN][1000 genomes]
rs28525101	0.81[ASN][1000 genomes]
rs28525658	0.95[ASN][1000 genomes]
rs28526077	0.88[ASN][1000 genomes]
rs28612609	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28626982	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28636605	0.95[ASN][1000 genomes]
rs28674185	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28751872	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28754336	0.98[ASN][1000 genomes]
rs28792801	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28826699	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28865976	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28875211	1.00[ASN][1000 genomes]
rs3813762	1.00[ASN][1000 genomes]
rs4239135	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4352086	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4791672	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4791673	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4791676	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4791678	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4792757	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4792760	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4792761	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4792762	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5000166	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55920274	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56303920	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57305125	0.95[EUR][1000 genomes]
rs57448521	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57694811	0.95[EUR][1000 genomes]
rs58164310	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59486407	0.98[ASN][1000 genomes]
rs59594997	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59826203	1.00[ASN][1000 genomes]
rs62072781	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072790	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62072792	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072845	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62073660	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502514	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208075	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7213274	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7217544	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217717	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7218241	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7219632	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221518	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7222622	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7222875	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7225641	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7226328	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72637355	0.95[ASN][1000 genomes]
rs72637356	1.00[ASN][1000 genomes]
rs72637357	1.00[ASN][1000 genomes]
rs72637358	1.00[ASN][1000 genomes]
rs72637359	0.98[ASN][1000 genomes]
rs72637360	0.98[ASN][1000 genomes]
rs72637361	0.85[ASN][1000 genomes]
rs72637362	0.87[ASN][1000 genomes]
rs72637363	0.83[ASN][1000 genomes]
rs8065558	1.00[ASN][1000 genomes]
rs8068349	0.98[ASN][1000 genomes]
rs8069286	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8074285	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074464	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074487	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8075988	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8076849	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8082225	0.98[ASN][1000 genomes]
rs8082323	0.95[EUR][1000 genomes]
rs8082462	0.95[EUR][1000 genomes]
rs8082650	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9890123	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9890698	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9891138	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9892170	0.85[EUR][1000 genomes]
rs9894637	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9898888	0.87[ASN][1000 genomes]
rs9899785	0.98[ASN][1000 genomes]
rs9899919	0.98[ASN][1000 genomes]
rs9901145	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9904901	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9905710	0.97[ASN][1000 genomes]
rs9906261	1.00[ASN][1000 genomes]
rs9906728	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9907785	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9908015	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9908390	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9909044	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9909955	0.99[ASN][1000 genomes]
rs9910087	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9910842	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9911162	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9911524	0.98[ASN][1000 genomes]
rs9911608	0.98[ASN][1000 genomes]
rs9911677	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9911820	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9911851	1.00[ASN][1000 genomes]
rs9915121	0.84[ASN][1000 genomes]
rs9916069	0.98[ASN][1000 genomes]
rs9916258	0.98[ASN][1000 genomes]
rs9916819	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
6	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	esv2758442	chr17:16527056-16817437	Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	esv2758676	chr17:16527056-16817437	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv427991	chr17:16527056-16817437	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16519800-16540000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr17:16522000-16540000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr17:16523000-16540400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr17:16523400-16537000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr17:16523400-16538400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr17:16524600-16539400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:16525800-16538200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr17:16525800-16538400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
9	chr17:16525800-16539800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:16527200-16542200	Weak transcription	Fetal Heart	heart
11	chr17:16527800-16535400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr17:16527800-16537000	Weak transcription	Psoas Muscle	Psoas
13	chr17:16527800-16556000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr17:16528000-16536000	Weak transcription	NH-A	brain
15	chr17:16528000-16537600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr17:16528000-16556000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr17:16528600-16535400	Weak transcription	Colon Smooth Muscle	Colon
18	chr17:16528600-16536800	Weak transcription	Fetal Brain Male	brain
19	chr17:16529000-16538000	Strong transcription	Fetal Lung	lung
20	chr17:16530000-16535000	Weak transcription	Fetal Kidney	kidney
21	chr17:16530000-16555400	Weak transcription	Small Intestine	intestine
22	chr17:16530200-16535000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr17:16530200-16540000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr17:16531000-16535200	Weak transcription	NHDF-Ad	bronchial
25	chr17:16531200-16535200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr17:16531200-16535600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
27	chr17:16531200-16538200	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr17:16531200-16556200	Weak transcription	Right Ventricle	heart
29	chr17:16531400-16535800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr17:16531600-16543800	Weak transcription	Stomach Mucosa	stomach
31	chr17:16531800-16538000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr17:16531800-16538200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr17:16531800-16556000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr17:16532000-16536600	Weak transcription	HSMM	muscle
35	chr17:16532000-16538200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr17:16532200-16535400	Strong transcription	Dnd41	blood
37	chr17:16532200-16536600	Weak transcription	Colonic Mucosa	Colon
38	chr17:16532200-16537600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr17:16532200-16538800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr17:16532200-16556000	Weak transcription	NHLF	lung
41	chr17:16532400-16556600	Weak transcription	Lung	lung
42	chr17:16532600-16535000	ZNF genes & repeats	Fetal Intestine Large	intestine
43	chr17:16532600-16537800	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr17:16532800-16537600	Strong transcription	Osteobl	bone
45	chr17:16532800-16538000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr17:16533000-16536600	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr17:16533000-16538000	Strong transcription	Adipose Nuclei	Adipose
48	chr17:16533000-16538400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
49	chr17:16533000-16539800	ZNF genes & repeats	A549	lung
50	chr17:16533200-16538600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links