Variant report

Variant	rs4774980
Chromosome Location	chr15:57983875-57983876
allele	A/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: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11071340	1.00[JPT][hapmap]
rs11071342	1.00[JPT][hapmap]
rs11854917	0.82[YRI][hapmap]
rs12440250	1.00[JPT][hapmap]
rs12441026	1.00[JPT][hapmap]
rs1593439	1.00[JPT][hapmap]
rs1834487	1.00[JPT][hapmap]
rs1946357	1.00[JPT][hapmap]
rs2018558	1.00[JPT][hapmap]
rs2081515	1.00[JPT][hapmap]
rs2414516	1.00[JPT][hapmap]
rs2470359	1.00[JPT][hapmap]
rs2899603	1.00[JPT][hapmap]
rs4564513	1.00[JPT][hapmap]
rs4774279	1.00[JPT][hapmap]
rs4774280	1.00[JPT][hapmap]
rs6493940	1.00[JPT][hapmap]
rs6493941	1.00[JPT][hapmap]
rs6493942	1.00[JPT][hapmap]
rs7181645	1.00[JPT][hapmap]
rs8023855	1.00[JPT][hapmap]
rs8024008	1.00[JPT][hapmap]
rs933839	1.00[JPT][hapmap]
rs9921015	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4774980	GCOM1,GRINL1A	cis	brain	BrainEAC

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	chr15:57973000-57984600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr15:57975600-57986600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:57975800-57986400	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:57977200-57984800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr15:57978400-57984600	Weak transcription	Fetal Stomach	stomach
7	chr15:57978400-57985000	Weak transcription	Fetal Intestine Large	intestine
8	chr15:57978800-57984400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:57979200-57984600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:57979200-57984600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr15:57979200-57986200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:57979200-57998200	Weak transcription	Fetal Intestine Small	intestine
13	chr15:57982200-57984600	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:57982400-57984000	Genic enhancers	Left Ventricle	heart
15	chr15:57982600-57984800	Enhancers	Pancreas	Pancrea
16	chr15:57982600-57984800	Enhancers	Right Atrium	heart
17	chr15:57982600-57986200	Enhancers	Hela-S3	cervix
18	chr15:57983200-57989400	Weak transcription	Lung	lung
19	chr15:57983400-57989000	Weak transcription	Aorta	Aorta
20	chr15:57983600-57984800	Enhancers	Gastric	stomach
21	chr15:57983600-57987800	Enhancers	Fetal Heart	heart
22	chr15:57983600-57998200	Weak transcription	Adipose Nuclei	Adipose
23	chr15:57983800-57984600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:57983800-57984600	Enhancers	Fetal Kidney	kidney
25	chr15:57983800-57984600	Weak transcription	Fetal Lung	lung
26	chr15:57983800-57984600	Weak transcription	Ovary	ovary
27	chr15:57983800-57986000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:57983800-57998400	Weak transcription	Right Ventricle	heart

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