Variant report

Variant	rs58253780
Chromosome Location	chr3:52051616-52051617
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52049402..52051939-chr3:52063118..52065044,2	K562	blood:
2	chr3:52048651..52051946-chr3:52056389..52059628,4	K562	blood:
3	chr3:52048651..52051918-chr3:52057028..52059628,3	K562	blood:
4	chr3:52050186..52052732-chr3:52065532..52068368,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11713678	1.00[AMR][1000 genomes]
rs60001415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60875614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964033	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964034	1.00[AMR][1000 genomes]
rs7627182	1.00[AMR][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	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	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52040800-52056000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:52046200-52058600	Enhancers	Spleen	Spleen
3	chr3:52046200-52060600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr3:52046600-52052000	Enhancers	Placenta	Placenta
5	chr3:52046800-52055400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:52047400-52051800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr3:52047600-52051800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr3:52048000-52056600	Enhancers	Right Ventricle	heart
9	chr3:52048600-52056600	Enhancers	Left Ventricle	heart
10	chr3:52048600-52056800	Enhancers	Psoas Muscle	Psoas
11	chr3:52048600-52061000	Enhancers	Fetal Muscle Leg	muscle
12	chr3:52048800-52051800	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr3:52049200-52052800	Weak transcription	Brain Anterior Caudate	brain
14	chr3:52049200-52055800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:52049400-52053600	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:52049800-52053400	Weak transcription	K562	blood
17	chr3:52049800-52053600	Weak transcription	GM12878-XiMat	blood
18	chr3:52049800-52055200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:52050000-52055600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:52050000-52056600	Enhancers	Right Atrium	heart
21	chr3:52050200-52052000	Enhancers	Brain Cingulate Gyrus	brain
22	chr3:52050200-52052000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:52050200-52052600	Enhancers	Stomach Smooth Muscle	stomach
24	chr3:52050200-52053200	Weak transcription	Fetal Intestine Small	intestine
25	chr3:52050600-52055400	Enhancers	Fetal Muscle Trunk	muscle
26	chr3:52050600-52073400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:52050800-52052000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:52050800-52052000	Enhancers	NHLF	lung
29	chr3:52050800-52052600	Weak transcription	Fetal Heart	heart
30	chr3:52050800-52053600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:52050800-52054600	Weak transcription	Lung	lung
32	chr3:52050800-52055600	Weak transcription	Fetal Brain Female	brain
33	chr3:52050800-52056000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:52051000-52052600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:52051200-52052000	Enhancers	NHDF-Ad	bronchial
36	chr3:52051200-52052800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:52051200-52053200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:52051200-52053600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:52051200-52056000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:52051400-52052000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:52051400-52055800	Weak transcription	Brain Angular Gyrus	brain
42	chr3:52051600-52051800	Enhancers	Fetal Brain Male	brain

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