Variant report

Variant	rs2854446
Chromosome Location	chr15:45353230-45353231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11634731	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2437866	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2467841	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2467843	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2470658	0.83[EUR][1000 genomes]
rs2470686	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35628479	0.81[EUR][1000 genomes]
rs3874239	0.82[EUR][1000 genomes]
rs4775707	0.82[ASN][1000 genomes]
rs58232764	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7165595	0.85[EUR][1000 genomes]
rs7167120	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	esv2757599	chr15:45100852-45383620	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv977710	chr15:45316191-45360995	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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
7	esv3438009	chr15:45329164-45353245	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region lncRNA	2 gene(s)	inside rSNPs	n/a
8	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2854446	CTD-2008A1.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2854446	RP11-109D20.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2854446	SORD	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45316600-45356600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:45316600-45366600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr15:45319200-45363200	Weak transcription	Fetal Thymus	thymus
4	chr15:45319800-45363600	Weak transcription	Brain Angular Gyrus	brain
5	chr15:45329400-45356400	Weak transcription	Osteobl	bone
6	chr15:45329800-45365800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:45331400-45369600	Weak transcription	Pancreas	Pancrea
8	chr15:45333400-45361200	Weak transcription	HUVEC	blood vessel
9	chr15:45337400-45365400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr15:45338000-45363800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr15:45338400-45365200	Weak transcription	HSMM	muscle
12	chr15:45340800-45359800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr15:45341200-45361800	Weak transcription	Ovary	ovary
14	chr15:45341200-45363600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:45341400-45353400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:45341400-45353400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr15:45341400-45362800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr15:45341600-45365800	Weak transcription	Fetal Lung	lung
19	chr15:45341800-45363000	Weak transcription	Gastric	stomach
20	chr15:45341800-45363200	Weak transcription	Brain Substantia Nigra	brain
21	chr15:45341800-45366600	Weak transcription	Thymus	Thymus
22	chr15:45342000-45361600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr15:45342000-45362400	Weak transcription	Fetal Brain Male	brain
24	chr15:45342800-45354400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr15:45342800-45363200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:45343200-45363400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr15:45343800-45353800	Weak transcription	NH-A	brain
28	chr15:45345000-45357800	Weak transcription	Fetal Stomach	stomach
29	chr15:45345000-45374800	Weak transcription	Aorta	Aorta
30	chr15:45345400-45369400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:45345600-45360400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr15:45345600-45364800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:45345800-45353800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:45345800-45357200	Weak transcription	Fetal Intestine Large	intestine
35	chr15:45345800-45359400	Weak transcription	Hela-S3	cervix
36	chr15:45345800-45361200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:45345800-45361600	Weak transcription	K562	blood
38	chr15:45345800-45361800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:45345800-45362000	Weak transcription	Fetal Kidney	kidney
40	chr15:45348400-45363200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:45348800-45354200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:45350200-45354400	Strong transcription	Liver	Liver
43	chr15:45350600-45353400	Weak transcription	Primary T cells from cord blood	blood
44	chr15:45350600-45356800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:45350600-45366400	Weak transcription	A549	lung
46	chr15:45350800-45353400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr15:45351000-45363400	Weak transcription	Brain Anterior Caudate	brain
48	chr15:45351000-45363600	Weak transcription	Primary B cells from cord blood	blood
49	chr15:45351200-45356600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr15:45351200-45363200	Weak transcription	Brain Hippocampus Middle	brain

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