Variant report

Variant	rs3909707
Chromosome Location	chr4:20677887-20677888
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1080123	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1080124	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13110741	0.86[ASN][1000 genomes]
rs13121188	0.87[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs13141509	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13147509	0.83[EUR][1000 genomes]
rs13148958	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13149131	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16869935	0.87[CEU][hapmap]
rs2195033	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34256982	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34354707	0.87[ASN][1000 genomes]
rs34733889	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34741188	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35192095	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35404532	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35469294	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3909706	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57152361	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59557053	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6830033	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71607029	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71607032	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71607034	0.83[EUR][1000 genomes]
rs7677916	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7696195	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs880855	0.88[ASN][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	nsv829875	chr4:20502895-20680956	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	89 gene(s)	inside rSNPs	diseases
2	nsv1013077	chr4:20599841-20732558	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3909707	C4orf28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20674000-20679000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr4:20674400-20678000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr4:20674400-20679000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr4:20674400-20684600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:20674600-20678000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:20674600-20681800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:20677600-20678000	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr4:20677600-20679400	Enhancers	Rectal Smooth Muscle	rectum
9	chr4:20677600-20679600	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr4:20677800-20678000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:20677800-20678400	Enhancers	Fetal Lung	lung
12	chr4:20677800-20678600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:20677800-20678800	Weak transcription	Colon Smooth Muscle	Colon

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