Variant report

Variant	rs4407312
Chromosome Location	chr20:23807028-23807029
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs4239738	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4332997	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4504066	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815228	0.82[AMR][1000 genomes]
rs6036531	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036540	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036548	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6049101	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049105	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049118	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049147	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6076126	0.82[AMR][1000 genomes]
rs6132660	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138126	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3349649	chr20:23689538-23834871	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3356621	chr20:23729388-23838883	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv458953	chr20:23731412-23808324	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv585727	chr20:23731412-23808324	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3377303	chr20:23746098-23827552	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv912823	chr20:23756139-23847009	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv436326	chr20:23757769-23838141	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv585729	chr20:23766096-23836124	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv965865	chr20:23784103-23836543	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv964415	chr20:23801700-23809333	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
12	nsv3336	chr20:23804081-23848943	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv833944	chr20:23806288-24021865	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4407312	MORN5	trans	parietal	SCAN
rs4407312	XRN2	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23804400-23807400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr20:23804800-23807400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:23806400-23807600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr20:23806400-23807800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr20:23806400-23807800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr20:23806600-23807400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr20:23806600-23807400	Enhancers	NHLF	lung
8	chr20:23806600-23807800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr20:23806800-23807400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr20:23806800-23807400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr20:23806800-23807400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr20:23806800-23807400	Enhancers	Fetal Muscle Leg	muscle
13	chr20:23806800-23807800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr20:23806800-23807800	Enhancers	NHDF-Ad	bronchial
15	chr20:23806800-23808000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr20:23806800-23808000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr20:23807000-23807400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr20:23807000-23807400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr20:23807000-23807400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr20:23807000-23807400	Enhancers	Fetal Muscle Trunk	muscle

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