Variant report

Variant	rs2470658
Chromosome Location	chr15:45344086-45344087
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11634731	0.91[EUR][1000 genomes]
rs12903829	0.92[ASN][1000 genomes]
rs2437866	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2467841	0.91[EUR][1000 genomes]
rs2467843	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2470686	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2854446	0.83[EUR][1000 genomes]
rs3874239	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58232764	0.83[EUR][1000 genomes]
rs7165595	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7167120	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv9260	chr15:45334818-45344949	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a
9	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2470658	CTD-2008A1.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2470658	CTD-2008A1.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2470658	SORD	cis	Skin Sun Exposed Lower leg	GTEx
rs2470658	RP11-109D20.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45316600-45344200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:45316600-45351000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr15:45316600-45356600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:45316600-45366600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:45316800-45346400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr15:45319200-45363200	Weak transcription	Fetal Thymus	thymus
7	chr15:45319800-45363600	Weak transcription	Brain Angular Gyrus	brain
8	chr15:45327600-45344400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:45329400-45356400	Weak transcription	Osteobl	bone
10	chr15:45329600-45350000	Weak transcription	A549	lung
11	chr15:45329800-45345600	Weak transcription	Fetal Kidney	kidney
12	chr15:45329800-45350200	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:45329800-45365800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:45331400-45369600	Weak transcription	Pancreas	Pancrea
15	chr15:45333400-45361200	Weak transcription	HUVEC	blood vessel
16	chr15:45336800-45347400	Weak transcription	Adipose Nuclei	Adipose
17	chr15:45337400-45365400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr15:45338000-45363800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr15:45338400-45365200	Weak transcription	HSMM	muscle
20	chr15:45338600-45345600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:45339000-45345800	Strong transcription	Liver	Liver
22	chr15:45339400-45345600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr15:45339800-45345600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:45340000-45345000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:45340000-45345800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
26	chr15:45340400-45345800	Strong transcription	Hela-S3	cervix
27	chr15:45340600-45345600	ZNF genes & repeats	Fetal Brain Female	brain
28	chr15:45340600-45345800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:45340600-45345800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
30	chr15:45340600-45345800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:45340600-45345800	ZNF genes & repeats	Dnd41	blood
32	chr15:45340800-45359800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr15:45341200-45345800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:45341200-45361800	Weak transcription	Ovary	ovary
35	chr15:45341200-45363600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:45341400-45349000	Weak transcription	Brain Anterior Caudate	brain
37	chr15:45341400-45353200	Weak transcription	Small Intestine	intestine
38	chr15:45341400-45353400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr15:45341400-45353400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr15:45341400-45362800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr15:45341600-45344400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:45341600-45344400	Weak transcription	Esophagus	oesophagus
43	chr15:45341600-45344800	Weak transcription	Aorta	Aorta
44	chr15:45341600-45348200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:45341600-45348200	Weak transcription	Fetal Heart	heart
46	chr15:45341600-45350400	Weak transcription	Left Ventricle	heart
47	chr15:45341600-45351400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:45341600-45365800	Weak transcription	Fetal Lung	lung
49	chr15:45341800-45344200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:45341800-45344400	Weak transcription	Fetal Stomach	stomach

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