Variant report

Variant	rs4687799
Chromosome Location	chr3:52069222-52069223
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52063916..52065862-chr3:52068496..52071263,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12487108	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12492696	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2334959	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2334960	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821841	0.82[AMR][1000 genomes]
rs4687606	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687798	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66514320	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs66530305	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6792935	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72622936	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72622937	0.81[AMR][1000 genomes]
rs745618	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
9	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52050600-52073400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:52062200-52073800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:52063600-52072400	Weak transcription	HSMM	muscle
4	chr3:52064400-52073600	Weak transcription	Spleen	Spleen
5	chr3:52066200-52071000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:52066400-52073600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:52067200-52072400	Weak transcription	Fetal Brain Female	brain
8	chr3:52067400-52069600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:52067400-52069800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:52067400-52069800	Weak transcription	Right Ventricle	heart
11	chr3:52067400-52071800	Weak transcription	Esophagus	oesophagus
12	chr3:52067400-52073400	Weak transcription	Left Ventricle	heart
13	chr3:52067600-52069600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:52067600-52072600	Weak transcription	Fetal Brain Male	brain
15	chr3:52067600-52072600	Weak transcription	Right Atrium	heart
16	chr3:52067600-52073600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:52067600-52073800	Weak transcription	Brain Germinal Matrix	brain
18	chr3:52067800-52069600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:52067800-52070000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:52067800-52070200	Weak transcription	Brain Anterior Caudate	brain
21	chr3:52067800-52070200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:52067800-52071400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:52067800-52071400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:52067800-52072800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:52068000-52069600	Weak transcription	Brain Angular Gyrus	brain
26	chr3:52068000-52070200	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:52068000-52070200	Weak transcription	Brain Substantia Nigra	brain
28	chr3:52068600-52070400	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:52068600-52074000	Weak transcription	Liver	Liver
30	chr3:52068800-52069600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
31	chr3:52068800-52073600	Enhancers	HepG2	liver
32	chr3:52069200-52072200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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