Variant report

Variant	rs58397909
Chromosome Location	chr15:75498001-75498002
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75497871-75498725	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:75496957-75499106	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr15:75496856-75499164	GM12892	blood:	n/a	n/a
4	POLR2A	chr15:75490585-75499135	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:75497998-75499191	GM12878	blood:	n/a	n/a
6	POLR2A	chr15:75496927-75499167	GM12891	blood:	n/a	n/a
7	POLR2A	chr15:75497875-75499173	GM12892	blood:	n/a	n/a
8	POLR2A	chr15:75497766-75498929	GM12891	blood:	n/a	n/a
9	WRNIP1	chr15:75495195-75498488	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:75489631-75513671	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:75314737..75326433-chr15:75490770..75500610,30	K562	blood:
2	chr15:75312886..75327225-chr15:75491522..75500922,36	K562	blood:
3	chr15:75314704..75323577-chr15:75491522..75500562,29	MCF-7	breast:
4	chr15:75334055..75342899-chr15:75492444..75498798,20	K562	blood:
5	chr15:75314427..75332274-chr15:75491598..75502885,56	MCF-7	breast:
6	chr15:75248197..75251380-chr15:75494107..75498676,4	MCF-7	breast:
7	chr15:75490684..75493339-chr15:75497415..75499804,2	K562	blood:
8	chr15:75331603..75340227-chr15:75492938..75499942,15	K562	blood:

No data

Variant related genes	Relation type
C15orf39	TF binding region
ENSG00000198794	Chromatin interaction
ENSG00000178718	Chromatin interaction
ENSG00000260483	Chromatin interaction
ENSG00000167173	Chromatin interaction
ENSG00000138621	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs28362067	1.00[AMR][1000 genomes]
rs57509570	1.00[AMR][1000 genomes]
rs57654778	1.00[AMR][1000 genomes]
rs58829645	0.91[AFR][1000 genomes]
rs59078717	1.00[AMR][1000 genomes]
rs73437018	1.00[AMR][1000 genomes]
rs73437030	1.00[AMR][1000 genomes]
rs73437031	1.00[AMR][1000 genomes]
rs73437042	1.00[AMR][1000 genomes]
rs73437054	1.00[AMR][1000 genomes]
rs73437055	1.00[AMR][1000 genomes]
rs73437074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73438811	1.00[AMR][1000 genomes]
rs8023648	1.00[AMR][1000 genomes]
rs8039385	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	nsv904383	chr15:75382542-75520378	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv1796196	chr15:75389382-75531124	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1039713	chr15:75394213-75674389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS 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	96 gene(s)	inside rSNPs	diseases
4	nsv1037713	chr15:75401213-75665304	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv1053212	chr15:75428467-75534408	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv833056	chr15:75452947-75614590	Enhancers Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv904384	chr15:75493823-75520378	Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv569995	chr15:75493823-75537475	Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv569996	chr15:75493823-75540491	Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS 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 target site	39 gene(s)	inside rSNPs	diseases
10	nsv904385	chr15:75493823-75546700	Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv482859	chr15:75493899-75688451	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75495800-75500000	Weak transcription	Brain Germinal Matrix	brain
2	chr15:75496000-75498200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr15:75496200-75498200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:75496200-75498600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr15:75496200-75498600	Weak transcription	Fetal Lung	lung
6	chr15:75496200-75506000	Weak transcription	Fetal Brain Female	brain
7	chr15:75496400-75498600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:75496400-75498800	Weak transcription	Small Intestine	intestine
9	chr15:75496400-75500400	Weak transcription	Right Atrium	heart
10	chr15:75496400-75504000	Weak transcription	HSMMtube	muscle
11	chr15:75496400-75506000	Weak transcription	Psoas Muscle	Psoas
12	chr15:75496600-75498200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:75496600-75498200	Enhancers	Right Ventricle	heart
14	chr15:75496600-75498200	Enhancers	Stomach Mucosa	stomach
15	chr15:75496600-75498400	Weak transcription	Aorta	Aorta
16	chr15:75496600-75498400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr15:75496600-75499600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:75496600-75499600	Weak transcription	HSMM	muscle
19	chr15:75496600-75501600	Weak transcription	Brain Substantia Nigra	brain
20	chr15:75496600-75506600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:75496800-75498200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:75496800-75498200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr15:75496800-75500400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr15:75496800-75507200	Weak transcription	NH-A	brain
25	chr15:75497000-75498200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:75497000-75498400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:75497200-75498200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:75497200-75498200	Enhancers	Adipose Nuclei	Adipose
29	chr15:75497200-75498200	Weak transcription	Esophagus	oesophagus
30	chr15:75497200-75498400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:75497200-75498400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:75497200-75500200	Weak transcription	Brain Anterior Caudate	brain
33	chr15:75497400-75498400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:75497400-75498400	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr15:75497600-75498200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:75497600-75498200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:75497600-75498200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr15:75497600-75498200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr15:75497600-75498200	Genic enhancers	Fetal Stomach	stomach
40	chr15:75497600-75498200	Weak transcription	Lung	lung
41	chr15:75497600-75498200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:75497600-75498400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:75497600-75498400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr15:75497600-75498400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:75497600-75498400	Weak transcription	Primary T cells from cord blood	blood
46	chr15:75497600-75498400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:75497600-75498400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:75497600-75498400	Weak transcription	Gastric	stomach
49	chr15:75497600-75498400	Weak transcription	Ovary	ovary
50	chr15:75497600-75498400	Weak transcription	Rectal Smooth Muscle	rectum

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