Variant report

Variant	rs59990341
Chromosome Location	chr15:31768964-31768965
allele	C/G
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: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10220758	1.00[EUR][1000 genomes]
rs12324344	1.00[EUR][1000 genomes]
rs1870438	1.00[EUR][1000 genomes]
rs57096428	1.00[EUR][1000 genomes]
rs58136622	1.00[EUR][1000 genomes]
rs58225563	1.00[EUR][1000 genomes]
rs58472566	1.00[EUR][1000 genomes]
rs58543954	1.00[EUR][1000 genomes]
rs58879698	1.00[EUR][1000 genomes]
rs59942460	1.00[EUR][1000 genomes]
rs60460548	1.00[EUR][1000 genomes]
rs60585254	1.00[EUR][1000 genomes]
rs60832561	1.00[EUR][1000 genomes]
rs61033035	1.00[EUR][1000 genomes]
rs61361220	1.00[AMR][1000 genomes]
rs61514382	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61741252	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73368664	1.00[EUR][1000 genomes]
rs73368676	1.00[AMR][1000 genomes]
rs73370522	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73370534	1.00[EUR][1000 genomes]
rs73370564	1.00[EUR][1000 genomes]
rs73372505	1.00[EUR][1000 genomes]
rs73372523	1.00[EUR][1000 genomes]
rs73372539	1.00[EUR][1000 genomes]
rs73372540	1.00[EUR][1000 genomes]
rs73372552	1.00[EUR][1000 genomes]
rs73372573	1.00[EUR][1000 genomes]
rs73372576	1.00[EUR][1000 genomes]
rs73372579	1.00[EUR][1000 genomes]
rs73372589	1.00[EUR][1000 genomes]
rs73372595	1.00[EUR][1000 genomes]
rs73372596	1.00[EUR][1000 genomes]
rs73374536	1.00[EUR][1000 genomes]
rs73374560	1.00[EUR][1000 genomes]
rs74010669	1.00[AMR][1000 genomes]
rs74010670	1.00[AMR][1000 genomes]
rs74010672	1.00[AMR][1000 genomes]
rs74012530	1.00[EUR][1000 genomes]
rs74012535	1.00[EUR][1000 genomes]
rs74012545	1.00[EUR][1000 genomes]
rs74012546	1.00[EUR][1000 genomes]
rs74012554	1.00[EUR][1000 genomes]
rs8029278	1.00[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:41 , 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	chr15:31766200-31770200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:31766200-31773600	Weak transcription	Small Intestine	intestine
13	chr15:31766200-31775000	Weak transcription	Left Ventricle	heart
14	chr15:31766400-31771000	Weak transcription	Colonic Mucosa	Colon
15	chr15:31766400-31772200	Weak transcription	Lung	lung
16	chr15:31766600-31771400	Weak transcription	Thymus	Thymus
17	chr15:31766600-31772000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:31766600-31772600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:31766600-31772600	Weak transcription	Fetal Thymus	thymus
20	chr15:31766600-31772800	Weak transcription	Spleen	Spleen
21	chr15:31766800-31772600	Weak transcription	Primary T cells from cord blood	blood
22	chr15:31766800-31774200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr15:31767000-31772200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:31767200-31772200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr15:31767200-31774200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr15:31767600-31770800	Weak transcription	Fetal Brain Female	brain
27	chr15:31767800-31772600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr15:31768000-31769200	Enhancers	HSMMtube	muscle
29	chr15:31768000-31772600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr15:31768000-31772600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr15:31768000-31773400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr15:31768200-31769000	Enhancers	Brain Cingulate Gyrus	brain
33	chr15:31768200-31769400	Enhancers	Fetal Muscle Leg	muscle
34	chr15:31768200-31772600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr15:31768200-31772800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:31768400-31774800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr15:31768600-31769000	Enhancers	Primary T cells fromperipheralblood	blood
38	chr15:31768600-31769000	Enhancers	Right Atrium	heart
39	chr15:31768600-31770800	Weak transcription	Fetal Lung	lung
40	chr15:31768800-31769000	Enhancers	Brain Substantia Nigra	brain
41	chr15:31768800-31769400	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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