Variant report

Variant	rs4687606
Chromosome Location	chr3:52064794-52064795
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52063916..52065862-chr3:52068496..52071263,2	MCF-7	breast:
2	chr3:52049402..52051939-chr3:52063118..52065044,2	K562	blood:
3	chr3:52064203..52066094-chr3:52088910..52090673,2	K562	blood:
4	chr3:52060421..52065315-chr3:52077239..52080916,4	K562	blood:
5	chr3:52037006..52039861-chr3:52064788..52067442,2	K562	blood:
6	chr3:52063546..52065859-chr3:52080631..52082453,2	MCF-7	breast:
7	chr3:52058192..52060960-chr3:52064469..52066894,2	K562	blood:
8	chr3:52063502..52067953-chr3:52083827..52087506,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000164086	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12487108	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12492696	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096104	0.80[AMR][1000 genomes]
rs2334959	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2334960	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3821841	0.83[AMR][1000 genomes]
rs4687798	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687799	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66514320	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66530305	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6792935	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72622936	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72622937	0.82[AMR][1000 genomes]
rs745618	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873175	0.80[AMR][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:40 , 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	chr3:52056600-52066400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:52060000-52065200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:52060600-52066000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:52061600-52068600	Enhancers	Fetal Muscle Leg	muscle
6	chr3:52062200-52073800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr3:52062400-52064800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:52062400-52065400	Enhancers	Psoas Muscle	Psoas
9	chr3:52062400-52065600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:52062400-52065600	Enhancers	NHEK	skin
11	chr3:52062400-52066000	Enhancers	HMEC	breast
12	chr3:52062600-52065600	Enhancers	Esophagus	oesophagus
13	chr3:52062800-52066800	Weak transcription	Fetal Brain Female	brain
14	chr3:52063000-52066600	Weak transcription	Fetal Brain Male	brain
15	chr3:52063000-52067800	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr3:52063200-52065800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:52063200-52066400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:52063200-52066800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:52063400-52066400	Weak transcription	Fetal Heart	heart
20	chr3:52063600-52065000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:52063600-52066000	Weak transcription	Brain Angular Gyrus	brain
22	chr3:52063600-52066000	Enhancers	Fetal Muscle Trunk	muscle
23	chr3:52063600-52066200	Weak transcription	Brain Anterior Caudate	brain
24	chr3:52063600-52066200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:52063600-52067600	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr3:52063600-52072400	Weak transcription	HSMM	muscle
27	chr3:52063800-52064800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:52063800-52064800	Weak transcription	Left Ventricle	heart
29	chr3:52063800-52065600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:52063800-52065600	Enhancers	HepG2	liver
31	chr3:52063800-52066600	Weak transcription	HSMMtube	muscle
32	chr3:52064000-52065000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:52064000-52065400	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:52064000-52065800	Weak transcription	Right Ventricle	heart
35	chr3:52064000-52067400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:52064400-52065400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:52064400-52073600	Weak transcription	Spleen	Spleen
38	chr3:52064600-52065000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:52064600-52065000	Weak transcription	Brain Substantia Nigra	brain
40	chr3:52064600-52065800	Weak transcription	Right Atrium	heart

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