Variant report

Variant	rs72892440
Chromosome Location	chr2:186290998-186290999
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10803984	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10931173	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10931174	0.80[EUR][1000 genomes]
rs10931175	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12151403	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12615022	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12990307	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13028718	0.94[ASN][1000 genomes]
rs1364483	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1477454	0.82[EUR][1000 genomes]
rs2042507	0.80[EUR][1000 genomes]
rs2370390	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66554560	0.96[ASN][1000 genomes]
rs67102416	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6712463	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6712480	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72892430	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9288115	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584009	chr2:186203397-186345148	Active TSS Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv459982	chr2:186213755-186475590	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv584012	chr2:186213755-186475590	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv875525	chr2:186223503-186434458	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv470502	chr2:186245653-186309738	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv459983	chr2:186245653-186377253	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv584013	chr2:186245653-186377253	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv524452	chr2:186258409-186297074	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv518379	chr2:186259653-186297074	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv875526	chr2:186272059-186434458	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv875527	chr2:186272059-186475590	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs72892440	AC007966.1	cis	Thyroid	GTEx
rs72892440	AC007966.1	cis	Heart Left Ventricle	GTEx
rs72892440	AC007966.1	cis	Stomach	GTEx
rs72892440	AC007966.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:186289600-186291200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:186289600-186291600	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr2:186289600-186291800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:186289600-186291800	Active TSS	H1 Cell Line	embryonic stem cell
5	chr2:186289600-186291800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr2:186289600-186291800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:186289600-186291800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:186289600-186291800	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr2:186289600-186292000	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr2:186289600-186292000	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr2:186289600-186292000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr2:186289600-186292200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:186289800-186291000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:186289800-186291400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:186289800-186292400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:186290000-186291200	Active TSS	Muscle Satellite Cultured Cells	--
17	chr2:186290200-186291000	Active TSS	Primary T cells from cord blood	blood
18	chr2:186290200-186291400	Active TSS	GM12878-XiMat	blood
19	chr2:186290200-186292000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr2:186290400-186291000	Active TSS	Fetal Intestine Large	intestine
21	chr2:186290800-186291000	Active TSS	HUES64 Cell Line	embryonic stem cell

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