Variant report

Variant	rs60409555
Chromosome Location	chr15:52234280-52234281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52232725..52234796-chr15:52242027..52243795,2	MCF-7	breast:
2	chr15:52215096..52217420-chr15:52231875..52234345,2	MCF-7	breast:
3	chr15:52230761..52232495-chr15:52232835..52234665,3	MCF-7	breast:
4	chr15:52232743..52235085-chr15:52238669..52241010,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2198804	1.00[AMR][1000 genomes]
rs28416491	0.94[ASN][1000 genomes]
rs3803365	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3985808	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs56903771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57897477	1.00[AMR][1000 genomes]
rs58370000	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58471786	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs58601413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59784585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60700084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1053788	chr15:52223389-52307138	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 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	chr15:52179600-52259800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:52194400-52236800	Weak transcription	Fetal Kidney	kidney
3	chr15:52194400-52239000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:52197000-52234800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:52200400-52262200	Weak transcription	Stomach Mucosa	stomach
6	chr15:52201000-52238800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:52204800-52238800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:52210000-52239000	Weak transcription	Colon Smooth Muscle	Colon
9	chr15:52211600-52237600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr15:52211600-52239200	Weak transcription	Right Ventricle	heart
11	chr15:52212400-52241600	Weak transcription	Small Intestine	intestine
12	chr15:52216000-52238600	Weak transcription	Pancreas	Pancrea
13	chr15:52217200-52238400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:52217200-52238800	Weak transcription	Brain Angular Gyrus	brain
15	chr15:52217600-52238800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:52217800-52237400	Weak transcription	Aorta	Aorta
17	chr15:52217800-52237400	Weak transcription	Brain Anterior Caudate	brain
18	chr15:52217800-52239000	Weak transcription	Gastric	stomach
19	chr15:52218000-52243200	Weak transcription	Fetal Heart	heart
20	chr15:52222600-52259800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:52222800-52236200	Strong transcription	Fetal Stomach	stomach
22	chr15:52223200-52245400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:52224000-52237400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:52224200-52237200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:52226000-52255200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:52226200-52234600	Strong transcription	Fetal Thymus	thymus
27	chr15:52226200-52242600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:52226200-52254800	Strong transcription	Thymus	Thymus
29	chr15:52226200-52255000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr15:52226200-52259400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:52226800-52237200	Weak transcription	Spleen	Spleen
32	chr15:52227000-52235600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:52227400-52234800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr15:52227400-52255000	Strong transcription	Liver	Liver
35	chr15:52227400-52258400	Strong transcription	Dnd41	blood
36	chr15:52227600-52235000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr15:52227800-52234800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr15:52227800-52234800	Strong transcription	Fetal Intestine Large	intestine
39	chr15:52227800-52255000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr15:52228200-52234600	Strong transcription	HepG2	liver
41	chr15:52228200-52235200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:52228400-52234800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:52228400-52238400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr15:52228600-52236400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr15:52229200-52237000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr15:52229200-52238200	Weak transcription	Brain Germinal Matrix	brain
47	chr15:52229400-52249000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr15:52229800-52254200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:52230000-52235000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr15:52230000-52237400	Weak transcription	Ovary	ovary

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