Variant report

Variant	rs58780990
Chromosome Location	chr3:50399434-50399435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50399404-50399456	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50398149..50400701-chr3:50422132..50425114,2	MCF-7	breast:
2	chr3:50397579..50400758-chr3:50401348..50405073,3	MCF-7	breast:
3	chr3:50386112..50390194-chr3:50392847..50399521,11	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYB561D2-2	chr3:50396941-50400230	NONHSAT089837

No data

Variant related genes	Relation type
ENSG00000271858	TF binding region
TMEM115	TF binding region
ENSG00000272104	Chromatin interaction
ENSG00000114395	Chromatin interaction
ENSG00000007402	Chromatin interaction
ENSG00000114388	Chromatin interaction
ENSG00000271858	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12485286	0.86[AFR][1000 genomes]
rs2233482	1.00[AMR][1000 genomes]
rs59556423	1.00[AMR][1000 genomes]
rs60983897	1.00[AMR][1000 genomes]
rs61275090	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61689858	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61737738	1.00[AMR][1000 genomes]
rs72932956	1.00[AMR][1000 genomes]
rs72932962	1.00[AMR][1000 genomes]
rs72932964	1.00[AMR][1000 genomes]
rs72932983	1.00[AMR][1000 genomes]
rs72932994	0.83[AFR][1000 genomes]
rs72934803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934809	0.93[AFR][1000 genomes]
rs72934811	0.86[AFR][1000 genomes]
rs72934814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934824	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934827	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934830	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs928946	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
6	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
7	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
9	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
10	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
11	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
12	nsv590256	chr3:50302830-50420554	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
13	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
14	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
15	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
16	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
17	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers 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 target site	55 gene(s)	inside rSNPs	diseases
18	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50397000-50401600	Weak transcription	Lung	lung
2	chr3:50397000-50402000	Weak transcription	Fetal Heart	heart
3	chr3:50397400-50401600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:50397400-50401600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr3:50397400-50401600	Weak transcription	Gastric	stomach
6	chr3:50397400-50401600	Weak transcription	Ovary	ovary
7	chr3:50397400-50401600	Weak transcription	Spleen	Spleen
8	chr3:50397400-50401800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:50397400-50401800	Weak transcription	Adipose Nuclei	Adipose
10	chr3:50397400-50401800	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:50397400-50401800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:50397400-50401800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:50397400-50401800	Weak transcription	Fetal Intestine Large	intestine
14	chr3:50397400-50401800	Weak transcription	Fetal Intestine Small	intestine
15	chr3:50397400-50401800	Weak transcription	Left Ventricle	heart
16	chr3:50397400-50401800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:50397400-50401800	Weak transcription	Stomach Mucosa	stomach
18	chr3:50397400-50401800	Weak transcription	Thymus	Thymus
19	chr3:50397400-50402000	Weak transcription	Right Atrium	heart
20	chr3:50397400-50402000	Weak transcription	Right Ventricle	heart
21	chr3:50397600-50400800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:50397600-50401400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:50397600-50401600	Weak transcription	Primary B cells from cord blood	blood
24	chr3:50397600-50401600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr3:50397600-50401600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:50397600-50401600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:50397600-50401600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:50397600-50401600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:50397600-50401600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:50397600-50401600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:50397600-50401600	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:50397600-50401600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:50397600-50401800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:50397600-50401800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:50397600-50401800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr3:50397600-50401800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:50397600-50401800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:50397600-50401800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:50397600-50401800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:50397600-50401800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:50397600-50401800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:50397600-50401800	Weak transcription	Colonic Mucosa	Colon
43	chr3:50397600-50401800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:50397600-50401800	Weak transcription	Fetal Lung	lung
45	chr3:50397600-50401800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:50397600-50401800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:50397600-50401800	Weak transcription	HUVEC	blood vessel
48	chr3:50397600-50402000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr3:50397600-50402000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:50397600-50402000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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