Variant report

Variant	rs72745565
Chromosome Location	chr15:57982811-57982812
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CGNL1-1	chr15:57982562-57984896	ENSG00000261699.1

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1009319	1.00[ASN][1000 genomes]
rs10152310	1.00[ASN][1000 genomes]
rs10152878	1.00[ASN][1000 genomes]
rs10851618	1.00[ASN][1000 genomes]
rs10851619	1.00[ASN][1000 genomes]
rs11071335	1.00[ASN][1000 genomes]
rs11852838	1.00[ASN][1000 genomes]
rs11853270	1.00[ASN][1000 genomes]
rs11854253	0.86[EUR][1000 genomes]
rs11854731	0.81[EUR][1000 genomes]
rs11856824	1.00[ASN][1000 genomes]
rs11857147	0.82[EUR][1000 genomes]
rs11858659	0.82[EUR][1000 genomes]
rs12323998	1.00[ASN][1000 genomes]
rs12324010	1.00[ASN][1000 genomes]
rs12324289	1.00[ASN][1000 genomes]
rs12324526	1.00[ASN][1000 genomes]
rs12442978	1.00[ASN][1000 genomes]
rs12442987	1.00[ASN][1000 genomes]
rs12443389	1.00[ASN][1000 genomes]
rs12443485	1.00[ASN][1000 genomes]
rs13380406	1.00[ASN][1000 genomes]
rs13380418	1.00[ASN][1000 genomes]
rs1346125	1.00[ASN][1000 genomes]
rs17239937	1.00[ASN][1000 genomes]
rs17820515	1.00[ASN][1000 genomes]
rs2172608	1.00[ASN][1000 genomes]
rs28421709	0.83[EUR][1000 genomes]
rs28557258	1.00[ASN][1000 genomes]
rs4774273	1.00[ASN][1000 genomes]
rs4774274	1.00[ASN][1000 genomes]
rs4774281	1.00[ASN][1000 genomes]
rs4774282	1.00[ASN][1000 genomes]
rs4774971	1.00[ASN][1000 genomes]
rs4774974	1.00[ASN][1000 genomes]
rs57589057	1.00[ASN][1000 genomes]
rs58017146	1.00[ASN][1000 genomes]
rs58919063	1.00[ASN][1000 genomes]
rs61600143	1.00[ASN][1000 genomes]
rs7178159	1.00[ASN][1000 genomes]
rs72743512	1.00[ASN][1000 genomes]
rs72743516	1.00[ASN][1000 genomes]
rs72745568	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72745576	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72745583	0.84[EUR][1000 genomes]
rs72745586	0.84[EUR][1000 genomes]
rs72745594	0.83[EUR][1000 genomes]
rs7359330	1.00[ASN][1000 genomes]
rs74016366	1.00[ASN][1000 genomes]
rs9796502	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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 target site	49 gene(s)	inside rSNPs	diseases
2	nsv530682	chr15:57912502-58108285	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer 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	8 gene(s)	inside rSNPs	diseases
3	nsv1038667	chr15:57933076-58481870	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv542400	chr15:57933076-58481870	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv3376567	chr15:57980485-57983033	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3421352	chr15:57980885-57983433	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57960800-57985000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr15:57968200-57983600	Weak transcription	Gastric	stomach
3	chr15:57973000-57984600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr15:57975600-57986600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:57975800-57986400	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:57977200-57984800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr15:57978200-57983600	Weak transcription	Spleen	Spleen
8	chr15:57978400-57983800	Weak transcription	Fetal Kidney	kidney
9	chr15:57978400-57984600	Weak transcription	Fetal Stomach	stomach
10	chr15:57978400-57985000	Weak transcription	Fetal Intestine Large	intestine
11	chr15:57978800-57984400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:57979200-57983200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr15:57979200-57984600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:57979200-57984600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr15:57979200-57986200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:57979200-57998200	Weak transcription	Fetal Intestine Small	intestine
17	chr15:57982200-57983600	Genic enhancers	Fetal Heart	heart
18	chr15:57982200-57984600	Weak transcription	Fetal Muscle Leg	muscle
19	chr15:57982400-57983000	Genic enhancers	Right Ventricle	heart
20	chr15:57982400-57983800	Enhancers	Ovary	ovary
21	chr15:57982400-57984000	Genic enhancers	Left Ventricle	heart
22	chr15:57982600-57983000	ZNF genes & repeats	Esophagus	oesophagus
23	chr15:57982600-57983000	ZNF genes & repeats	Lung	lung
24	chr15:57982600-57983600	Strong transcription	Adipose Nuclei	Adipose
25	chr15:57982600-57984800	Enhancers	Pancreas	Pancrea
26	chr15:57982600-57984800	Enhancers	Right Atrium	heart
27	chr15:57982600-57986200	Enhancers	Hela-S3	cervix
28	chr15:57982800-57983400	Enhancers	Aorta	Aorta

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