Variant report

Variant	rs4459919
Chromosome Location	chr3:90134010-90134011
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11926877	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11927254	1.00[AMR][1000 genomes]
rs1402832	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55958954	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56978342	0.83[AMR][1000 genomes]
rs57268246	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs57403980	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57742239	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs57945456	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs57953580	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58016519	0.83[AMR][1000 genomes]
rs59297554	0.89[AFR][1000 genomes]
rs59437743	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59827615	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs60383922	0.97[AFR][1000 genomes]
rs60834002	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61580714	0.82[AFR][1000 genomes]
rs6551442	0.83[AMR][1000 genomes]
rs6551443	0.83[AMR][1000 genomes]
rs6551452	1.00[AFR][1000 genomes]
rs6789123	0.89[AFR][1000 genomes]
rs6789628	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6807535	0.83[AMR][1000 genomes]
rs72917689	0.83[AMR][1000 genomes]
rs72921826	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72921827	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72921828	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72923795	0.88[AFR][1000 genomes]
rs72923797	0.97[AFR][1000 genomes]
rs72923801	0.83[AFR][1000 genomes]
rs7651366	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008018	chr3:89382031-90254063	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv536639	chr3:89382031-90254063	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1010932	chr3:89424428-90192503	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1010021	chr3:89521983-90141988	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv530024	chr3:89548440-90304841	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1008130	chr3:89837442-90192503	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1010796	chr3:89870548-90192503	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1013598	chr3:89879377-90192503	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv536642	chr3:89879377-90192503	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv590966	chr3:89904882-90199759	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1007523	chr3:89951855-90144385	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1011581	chr3:89951855-90144746	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv997583	chr3:89951855-90154534	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1006665	chr3:89958844-90162193	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv998541	chr3:89961515-90153365	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv536643	chr3:89961515-90153365	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv590967	chr3:89979895-90138312	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv590968	chr3:89979895-90199759	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv460761	chr3:89987871-90138312	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv590969	chr3:89987871-90138312	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv590970	chr3:89987871-90441306	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv1010292	chr3:90057464-90192503	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:90132200-90134400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr3:90132200-90136000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:90132400-90134400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr3:90132400-90135400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:90132600-90135200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr3:90132600-90135400	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
7	chr3:90132800-90136600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
8	chr3:90133400-90135200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:90133400-90135400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:90133600-90134600	Weak transcription	Stomach Mucosa	stomach
11	chr3:90133800-90134600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:90133800-90138600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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