Variant report

Variant	rs59280971
Chromosome Location	chr10:698136-698137
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C10orf108-1	chr10:697051-698595	NONHSAT010867

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10752016	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10904534	0.82[ASN][1000 genomes]
rs10904536	0.83[ASN][1000 genomes]
rs10904537	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253283	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11253284	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11253289	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11253290	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11253291	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11253292	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253293	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253308	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253315	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11253316	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17136372	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2034851	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2085346	0.81[EUR][1000 genomes]
rs28971758	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3750730	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3750731	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853287	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853288	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3853290	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4369323	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4880737	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4881499	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4881500	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4881503	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4881504	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61676960	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61833033	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs705486	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7076929	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7077311	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7919597	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs883728	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036501	chr10:224406-775824	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1052660	chr10:224406-785929	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1043752	chr10:224406-789665	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv916363	chr10:224406-816628	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers 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	38 gene(s)	inside rSNPs	diseases
6	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv1035580	chr10:248463-832240	Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv540392	chr10:248463-832240	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv549751	chr10:313304-734229	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers 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	15 gene(s)	inside rSNPs	diseases
10	nsv1050252	chr10:375035-839594	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv540397	chr10:375035-839594	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
12	nsv1036348	chr10:387880-817037	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
13	nsv1035712	chr10:436747-714987	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1048859	chr10:442805-887622	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
15	nsv1039958	chr10:450753-889167	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
16	nsv540400	chr10:450753-889167	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
17	nsv549753	chr10:458477-894838	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
18	nsv868946	chr10:503401-816628	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
19	nsv1039849	chr10:535309-829217	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
20	nsv915560	chr10:536704-816628	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
21	nsv916839	chr10:536707-817076	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
22	nsv894707	chr10:552355-752193	Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
23	nsv1044857	chr10:577396-856059	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
24	nsv540402	chr10:577396-856059	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
25	nsv528733	chr10:577444-838378	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
26	nsv1036675	chr10:600206-839594	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
27	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
28	esv1801137	chr10:626412-735901	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
29	nsv894714	chr10:626782-734229	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
30	nsv1042115	chr10:641343-825145	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
31	nsv540405	chr10:641343-825145	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
32	nsv549764	chr10:671495-704460	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
33	nsv825205	chr10:677475-804402	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
34	nsv825206	chr10:688018-818192	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
35	nsv975002	chr10:691542-699487	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
36	esv1850995	chr10:696237-735901	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:672000-700000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr10:684200-700000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr10:685600-699800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr10:687400-700000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr10:688800-698200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr10:688800-702600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr10:691200-704200	Weak transcription	HSMM	muscle
8	chr10:691200-704800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr10:691400-704200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr10:695600-698400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr10:695600-699200	Enhancers	Fetal Brain Male	brain
12	chr10:695800-698800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr10:695800-699000	Enhancers	Fetal Muscle Leg	muscle
14	chr10:695800-699200	Enhancers	Fetal Muscle Trunk	muscle
15	chr10:696000-698400	Enhancers	Brain Germinal Matrix	brain
16	chr10:696200-699800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr10:696200-703000	Enhancers	Brain Cingulate Gyrus	brain
18	chr10:696400-698200	Enhancers	Spleen	Spleen
19	chr10:696600-699600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr10:696600-699800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr10:696600-699800	Enhancers	Brain Angular Gyrus	brain
22	chr10:696600-700000	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr10:696600-701800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr10:696800-698600	Enhancers	Ovary	ovary
25	chr10:696800-699200	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr10:696800-700000	Enhancers	Brain Substantia Nigra	brain
27	chr10:696800-700400	Enhancers	Brain Anterior Caudate	brain
28	chr10:696800-700600	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr10:696800-702400	Weak transcription	Small Intestine	intestine
30	chr10:697000-698800	Enhancers	Fetal Brain Female	brain
31	chr10:697000-699200	Enhancers	Pancreas	Pancrea
32	chr10:697000-699800	Enhancers	Brain Hippocampus Middle	brain
33	chr10:697200-698200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr10:697200-698200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr10:697200-698200	Weak transcription	Right Atrium	heart
36	chr10:697200-698400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr10:697200-698400	Genic enhancers	Fetal Intestine Small	intestine
38	chr10:697200-699000	Enhancers	Right Ventricle	heart
39	chr10:697200-699200	Enhancers	Left Ventricle	heart
40	chr10:697200-700200	Weak transcription	Fetal Lung	lung
41	chr10:697200-701200	Weak transcription	Aorta	Aorta
42	chr10:697200-704400	Weak transcription	Liver	Liver
43	chr10:697200-705200	Weak transcription	NHLF	lung
44	chr10:697400-698200	Weak transcription	Gastric	stomach
45	chr10:697400-699200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr10:697400-699400	Weak transcription	Adipose Nuclei	Adipose
47	chr10:697400-699800	Weak transcription	Colonic Mucosa	Colon
48	chr10:697400-699800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr10:697400-699800	Weak transcription	Stomach Mucosa	stomach
50	chr10:697400-700000	Weak transcription	Fetal Stomach	stomach

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