Variant report

Variant	rs13410391
Chromosome Location	chr2:48757823-48757824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STON1-1	chr2:48757737-48757968	NONHSAT070624
2	lnc-STON1-1	chr2:48757019-48759056	NONHSAT070625

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10184783	0.88[ASN][1000 genomes]
rs12616834	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12618125	0.94[EUR][1000 genomes]
rs12620002	0.82[ASN][1000 genomes]
rs2177487	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2177488	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34461314	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4293602	0.86[CHB][hapmap]
rs4296472	0.80[ASN][1000 genomes]
rs4497915	0.82[JPT][hapmap]
rs4528813	0.92[EUR][1000 genomes]
rs4641991	0.92[EUR][1000 genomes]
rs4952914	0.86[EUR][1000 genomes]
rs4953587	0.92[EUR][1000 genomes]
rs6545047	0.94[EUR][1000 genomes]
rs6733533	0.95[ASN][1000 genomes]
rs6754946	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1007491	chr2:48752185-48796441	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv535683	chr2:48752185-48796441	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3390375	chr2:48755948-48758496	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3359548	chr2:48756073-48758621	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13410391	CCDC128	Cis_1M	lymphoblastoid	RTeQTL
rs13410391	PPP1R21	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48756400-48758000	Enhancers	Fetal Brain Male	brain
2	chr2:48756400-48758000	Flanking Active TSS	Dnd41	blood
3	chr2:48756400-48758600	Active TSS	Fetal Kidney	kidney
4	chr2:48756400-48759000	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr2:48756600-48758000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr2:48756600-48758000	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr2:48756600-48758000	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr2:48756600-48758200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr2:48756600-48758400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr2:48756600-48758600	Active TSS	Fetal Lung	lung
11	chr2:48756600-48758800	Active TSS	H9 Cell Line	embryonic stem cell
12	chr2:48756600-48758800	Active TSS	Duodenum Mucosa	Duodenum
13	chr2:48756600-48759000	Active TSS	Colon Smooth Muscle	Colon
14	chr2:48756600-48759000	Active TSS	Fetal Brain Female	brain
15	chr2:48756600-48759800	Active TSS	Stomach Smooth Muscle	stomach
16	chr2:48756800-48758000	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr2:48756800-48758000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:48756800-48758000	Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr2:48756800-48758000	Active TSS	Placenta Amnion	Placenta Amnion
20	chr2:48756800-48758000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
21	chr2:48756800-48758200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:48756800-48758200	Active TSS	Primary T cells from cord blood	blood
23	chr2:48756800-48758200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr2:48756800-48758200	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr2:48756800-48758400	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr2:48756800-48758400	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr2:48756800-48758600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:48756800-48758600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:48756800-48758600	Active TSS	NHDF-Ad	bronchial
30	chr2:48756800-48758600	Active TSS	NHLF	lung
31	chr2:48756800-48758800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:48756800-48758800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:48756800-48758800	Active TSS	Brain Angular Gyrus	brain
34	chr2:48756800-48758800	Active TSS	Brain Anterior Caudate	brain
35	chr2:48756800-48758800	Active TSS	Brain Substantia Nigra	brain
36	chr2:48756800-48758800	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr2:48756800-48758800	Active TSS	Left Ventricle	heart
38	chr2:48756800-48758800	Active TSS	Lung	lung
39	chr2:48756800-48759000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:48756800-48759000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:48756800-48759000	Active TSS	Aorta	Aorta
42	chr2:48756800-48759000	Active TSS	Brain Hippocampus Middle	brain
43	chr2:48756800-48759000	Active TSS	Rectal Smooth Muscle	rectum
44	chr2:48756800-48759200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:48756800-48759200	Active TSS	Fetal Stomach	stomach
46	chr2:48756800-48759200	Active TSS	Ovary	ovary
47	chr2:48756800-48759800	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr2:48757000-48758000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:48757000-48758200	Active TSS	Muscle Satellite Cultured Cells	--
50	chr2:48757000-48758200	Active TSS	Fetal Muscle Leg	muscle

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