Variant report

Variant	rs9994859
Chromosome Location	chr4:90590704-90590705
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10000914	0.88[ASN][1000 genomes]
rs10001007	0.87[ASN][1000 genomes]
rs10012402	0.88[ASN][1000 genomes]
rs10012586	0.88[ASN][1000 genomes]
rs10012803	0.87[ASN][1000 genomes]
rs10018310	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10023171	0.87[ASN][1000 genomes]
rs10213062	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12502730	0.88[ASN][1000 genomes]
rs12510321	0.88[ASN][1000 genomes]
rs17015961	0.95[ASN][1000 genomes]
rs17015968	0.95[ASN][1000 genomes]
rs28408495	0.88[ASN][1000 genomes]
rs28437605	0.88[ASN][1000 genomes]
rs28459090	0.88[ASN][1000 genomes]
rs28473552	0.87[ASN][1000 genomes]
rs28498646	0.95[ASN][1000 genomes]
rs28505526	0.88[ASN][1000 genomes]
rs28550468	0.88[ASN][1000 genomes]
rs28667466	0.87[ASN][1000 genomes]
rs28684694	0.87[ASN][1000 genomes]
rs28709174	0.85[ASN][1000 genomes]
rs3846288	0.96[ASN][1000 genomes]
rs57856896	0.95[ASN][1000 genomes]
rs60954064	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674594	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7674641	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7683289	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9986016	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9986065	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv879534	chr4:90498133-90591889	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
6	nsv879535	chr4:90565218-90624853	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
7	nsv461578	chr4:90572322-90624853	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
8	nsv461579	chr4:90572322-90624853	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
9	nsv594818	chr4:90572322-90624853	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
10	nsv461580	chr4:90572322-90630901	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
11	nsv594819	chr4:90572322-90630901	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
12	esv3496349	chr4:90576823-90603051	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a
13	esv3496350	chr4:90576823-90603051	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a
14	esv3488491	chr4:90579229-90593527	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	lncRNA	n/a	inside rSNPs	n/a
15	nsv594820	chr4:90579586-90600198	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a
16	esv3488493	chr4:90579679-90593277	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	lncRNA	n/a	inside rSNPs	n/a
17	esv3488490	chr4:90580296-90592350	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	inside rSNPs	n/a
18	esv3488492	chr4:90580306-90592339	Enhancers Weak transcription Flanking Active TSS	lncRNA	n/a	inside rSNPs	n/a
19	esv3488489	chr4:90580337-90592308	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	inside rSNPs	n/a
20	esv3488494	chr4:90580337-90592308	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	inside rSNPs	n/a
21	esv14771	chr4:90580433-90592288	Enhancers Weak transcription Flanking Active TSS	lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90577800-90602600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:90582600-90602600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:90587000-90592400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:90587200-90602600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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