Variant report

Variant	rs60539260
Chromosome Location	chr13:53019556-53019557
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:53017677..53022269-chr13:53022442..53026165,6	MCF-7	breast:
2	chr13:53015538..53018877-chr13:53019093..53022544,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136100	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs55645852	0.82[AFR][1000 genomes]
rs55796806	0.94[AFR][1000 genomes]
rs55924773	0.82[AFR][1000 genomes]
rs56116089	0.82[AFR][1000 genomes]
rs56252739	0.82[AFR][1000 genomes]
rs57214011	0.82[AFR][1000 genomes]
rs58762975	0.82[AFR][1000 genomes]
rs60864284	0.82[AFR][1000 genomes]
rs74085745	0.82[AFR][1000 genomes]
rs74085746	0.82[AFR][1000 genomes]
rs74085748	0.82[AFR][1000 genomes]
rs74085750	0.82[AFR][1000 genomes]
rs74085767	0.82[AFR][1000 genomes]
rs74085776	0.82[AFR][1000 genomes]
rs74085781	0.82[AFR][1000 genomes]
rs74085783	0.94[AFR][1000 genomes]
rs74085795	0.82[AFR][1000 genomes]
rs74085799	0.82[AFR][1000 genomes]
rs74087304	0.82[AFR][1000 genomes]
rs74087342	0.94[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS 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 target site	35 gene(s)	inside rSNPs	diseases
5	nsv900084	chr13:52835231-53119704	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1838257	chr13:52971893-53231454	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv3434605	chr13:52999509-53034851	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52980200-53021600	Weak transcription	Small Intestine	intestine
2	chr13:52981000-53022800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr13:52984400-53023400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr13:52987200-53023600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr13:52989000-53021600	Weak transcription	Fetal Heart	heart
6	chr13:52989000-53022800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:52995200-53023800	Weak transcription	Aorta	Aorta
8	chr13:52995800-53019800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr13:52995800-53023800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr13:52999000-53022400	Weak transcription	Right Ventricle	heart
11	chr13:53000600-53022200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr13:53001800-53022200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr13:53003800-53021600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr13:53003800-53021600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr13:53003800-53021600	Weak transcription	Right Atrium	heart
16	chr13:53003800-53022000	Weak transcription	Brain Substantia Nigra	brain
17	chr13:53003800-53022400	Weak transcription	Psoas Muscle	Psoas
18	chr13:53008600-53019600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr13:53008600-53023600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr13:53008800-53021800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr13:53008800-53022200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr13:53009200-53022400	Weak transcription	Brain Germinal Matrix	brain
23	chr13:53010200-53022800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr13:53010600-53021600	Weak transcription	Esophagus	oesophagus
25	chr13:53010600-53021800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr13:53010600-53022200	Weak transcription	Stomach Mucosa	stomach
27	chr13:53011400-53021600	Weak transcription	A549	lung
28	chr13:53013000-53021600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr13:53013000-53021600	Weak transcription	Hela-S3	cervix
30	chr13:53013200-53022200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr13:53013200-53022400	Weak transcription	Fetal Brain Male	brain
32	chr13:53013400-53020400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr13:53013400-53021600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr13:53013400-53021600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr13:53013400-53021600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr13:53013400-53021600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr13:53013400-53022200	Weak transcription	Brain Angular Gyrus	brain
38	chr13:53013400-53022800	Weak transcription	NHLF	lung
39	chr13:53013400-53023400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr13:53013600-53020400	Weak transcription	K562	blood
41	chr13:53013800-53021600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr13:53014800-53022600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr13:53015400-53021600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr13:53015400-53021600	Weak transcription	Fetal Lung	lung
45	chr13:53015400-53021600	Weak transcription	Spleen	Spleen
46	chr13:53015400-53022200	Weak transcription	Fetal Brain Female	brain
47	chr13:53015400-53022200	Weak transcription	Gastric	stomach
48	chr13:53015400-53022200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr13:53015400-53023200	Weak transcription	Colonic Mucosa	Colon
50	chr13:53015400-53023400	Weak transcription	Fetal Kidney	kidney

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