Variant report

Variant	rs11764799
Chromosome Location	chr7:48078055-48078056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10247913	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10253220	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10253238	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10256256	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10261930	0.91[EUR][1000 genomes]
rs10951937	0.84[EUR][1000 genomes]
rs10951938	0.84[EUR][1000 genomes]
rs10951940	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10951941	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10951942	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11761275	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11762077	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11766144	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11766891	0.94[EUR][1000 genomes]
rs11767002	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11768277	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11772387	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11772633	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11773348	0.83[EUR][1000 genomes]
rs12535580	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12702405	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12702406	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1318327	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13230023	0.84[EUR][1000 genomes]
rs1574242	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1915960	0.94[EUR][1000 genomes]
rs1915962	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1915966	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1915967	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1915968	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1915971	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1915972	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2037482	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2348666	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2348667	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2348670	0.84[EUR][1000 genomes]
rs2686783	0.81[EUR][1000 genomes]
rs2881991	0.89[EUR][1000 genomes]
rs2881992	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4332046	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4354227	0.81[AMR][1000 genomes]
rs4618593	0.85[EUR][1000 genomes]
rs6978838	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6979699	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7357251	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7357327	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7456745	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7779252	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7791084	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7791572	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7791823	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7807611	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7807612	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7807654	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7807750	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7808462	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9690905	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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv888004	chr7:48028771-48120717	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11764799	C7orf57	cis	Esophagus Mucosa	GTEx
rs11764799	UPP1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48076200-48079600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:48076200-48079600	Weak transcription	HMEC	breast
3	chr7:48076200-48079600	Weak transcription	NHEK	skin
4	chr7:48076200-48080600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:48076200-48080800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:48077400-48078200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
7	chr7:48077600-48078200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
8	chr7:48077600-48078400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr7:48077800-48078200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr7:48078000-48078200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr7:48078000-48078200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:48078000-48080000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr7:48078000-48081000	Enhancers	H9 Cell Line	embryonic stem cell

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