Variant report

Variant	rs1017720
Chromosome Location	chr15:31768529-31768530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OTUD7A-1	chr15:31767607-31770705	NONHSAT041463

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1077169	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10851568	0.83[EUR][1000 genomes]
rs10851569	0.83[EUR][1000 genomes]
rs11071070	0.83[EUR][1000 genomes]
rs11071075	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11071076	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12148161	0.80[EUR][1000 genomes]
rs12148181	0.83[EUR][1000 genomes]
rs12439195	0.83[EUR][1000 genomes]
rs12439214	0.82[EUR][1000 genomes]
rs12439216	0.82[EUR][1000 genomes]
rs12439310	0.83[ASN][1000 genomes]
rs12440316	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12441529	0.83[EUR][1000 genomes]
rs12441588	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12441627	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12443255	0.84[EUR][1000 genomes]
rs12443432	0.83[EUR][1000 genomes]
rs12592099	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12592342	0.83[GIH][hapmap]
rs12592371	0.82[EUR][1000 genomes]
rs12595455	0.82[EUR][1000 genomes]
rs1380235	0.82[EUR][1000 genomes]
rs17228303	0.82[EUR][1000 genomes]
rs17228317	0.83[EUR][1000 genomes]
rs17815977	0.83[EUR][1000 genomes]
rs2008020	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2125617	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2125618	0.84[EUR][1000 genomes]
rs2219508	0.93[GIH][hapmap];0.80[MEX][hapmap];0.82[EUR][1000 genomes]
rs2338680	0.85[JPT][hapmap]
rs2338683	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28366602	0.82[EUR][1000 genomes]
rs28367155	0.82[EUR][1000 genomes]
rs28379435	0.82[EUR][1000 genomes]
rs28392564	0.83[EUR][1000 genomes]
rs28403178	0.84[EUR][1000 genomes]
rs28421719	0.82[EUR][1000 genomes]
rs28470561	0.83[EUR][1000 genomes]
rs28533482	0.83[EUR][1000 genomes]
rs28549906	0.83[EUR][1000 genomes]
rs28557161	0.83[EUR][1000 genomes]
rs28579624	0.82[EUR][1000 genomes]
rs28619436	0.81[EUR][1000 genomes]
rs28623261	0.82[EUR][1000 genomes]
rs28633343	0.82[EUR][1000 genomes]
rs28633823	0.83[EUR][1000 genomes]
rs28644187	0.82[EUR][1000 genomes]
rs28655541	0.83[EUR][1000 genomes]
rs28668028	0.83[EUR][1000 genomes]
rs28673491	0.83[EUR][1000 genomes]
rs28683761	0.83[EUR][1000 genomes]
rs28685794	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28687203	0.83[EUR][1000 genomes]
rs28696791	0.83[EUR][1000 genomes]
rs28703622	0.83[EUR][1000 genomes]
rs28716634	0.82[EUR][1000 genomes]
rs4497646	0.83[EUR][1000 genomes]
rs4779528	0.83[GIH][hapmap]
rs4779529	0.82[EUR][1000 genomes]
rs4779530	0.82[EUR][1000 genomes]
rs4779534	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4779882	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55806858	0.83[EUR][1000 genomes]
rs56008248	0.83[EUR][1000 genomes]
rs56332002	0.81[EUR][1000 genomes]
rs56349550	0.83[EUR][1000 genomes]
rs62037907	0.82[EUR][1000 genomes]
rs6493688	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493689	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7403275	0.82[EUR][1000 genomes]
rs7403458	0.82[EUR][1000 genomes]
rs755809	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs755812	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8023660	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8023664	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8023790	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8035018	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8038667	0.82[EUR][1000 genomes]
rs8038953	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8040186	0.83[EUR][1000 genomes]
rs971330	0.82[EUR][1000 genomes]
rs971331	0.82[EUR][1000 genomes]
rs971332	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv903840	chr15:31589970-31800149	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1051589	chr15:31728004-31972706	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv542320	chr15:31728004-31972706	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv469633	chr15:31731003-31904613	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv482330	chr15:31731003-31904613	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv903844	chr15:31736091-31781988	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1046271	chr15:31741255-31795961	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv903845	chr15:31751664-31939001	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv1803983	chr15:31760986-31776503	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31758200-31774800	Weak transcription	Gastric	stomach
2	chr15:31758200-31775400	Weak transcription	Pancreas	Pancrea
3	chr15:31763200-31771200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:31765400-31773000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:31765400-31773000	Weak transcription	Fetal Heart	heart
6	chr15:31765600-31770800	Weak transcription	Fetal Brain Male	brain
7	chr15:31765600-31775200	Weak transcription	Brain Anterior Caudate	brain
8	chr15:31765600-31779200	Weak transcription	Brain Angular Gyrus	brain
9	chr15:31765800-31775400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:31766000-31776400	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:31766200-31768600	Weak transcription	Right Atrium	heart
12	chr15:31766200-31770200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:31766200-31773600	Weak transcription	Small Intestine	intestine
14	chr15:31766200-31775000	Weak transcription	Left Ventricle	heart
15	chr15:31766400-31771000	Weak transcription	Colonic Mucosa	Colon
16	chr15:31766400-31772200	Weak transcription	Lung	lung
17	chr15:31766600-31771400	Weak transcription	Thymus	Thymus
18	chr15:31766600-31772000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:31766600-31772600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:31766600-31772600	Weak transcription	Fetal Thymus	thymus
21	chr15:31766600-31772800	Weak transcription	Spleen	Spleen
22	chr15:31766800-31768600	Enhancers	Fetal Lung	lung
23	chr15:31766800-31772600	Weak transcription	Primary T cells from cord blood	blood
24	chr15:31766800-31774200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:31767000-31772200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr15:31767200-31772200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:31767200-31774200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr15:31767400-31768600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr15:31767600-31770800	Weak transcription	Fetal Brain Female	brain
30	chr15:31767800-31772600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr15:31768000-31768600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:31768000-31768600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr15:31768000-31769200	Enhancers	HSMMtube	muscle
34	chr15:31768000-31772600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr15:31768000-31772600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr15:31768000-31773400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr15:31768200-31769000	Enhancers	Brain Cingulate Gyrus	brain
38	chr15:31768200-31769400	Enhancers	Fetal Muscle Leg	muscle
39	chr15:31768200-31772600	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr15:31768200-31772800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr15:31768400-31768800	Weak transcription	Brain Substantia Nigra	brain
42	chr15:31768400-31768800	Enhancers	Esophagus	oesophagus
43	chr15:31768400-31768800	Enhancers	Fetal Muscle Trunk	muscle
44	chr15:31768400-31774800	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links