Variant report

Variant	rs6493553
Chromosome Location	chr15:52620573-52620574
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52580244..52584410-chr15:52619433..52625902,7	MCF-7	breast:
2	chr15:52620021..52622500-chr15:52969872..52972000,2	MCF-7	breast:
3	chr15:52586610..52588635-chr15:52620259..52623836,3	MCF-7	breast:
4	chr15:52618630..52620915-chr15:52624635..52627078,2	MCF-7	breast:
5	chr15:52620335..52622038-chr15:52622788..52624501,2	K562	blood:
6	chr15:52586491..52591216-chr15:52616639..52620986,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128833	Chromatin interaction
ENSG00000047346	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10444828	1.00[EUR][1000 genomes]
rs12906271	1.00[MKK][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12910858	1.00[EUR][1000 genomes]
rs12914306	1.00[EUR][1000 genomes]
rs12914548	1.00[EUR][1000 genomes]
rs2414136	0.80[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414140	0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414149	1.00[EUR][1000 genomes]
rs2693460	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs28421476	1.00[EUR][1000 genomes]
rs2924130	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs4238391	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7183258	1.00[EUR][1000 genomes]
rs73404874	1.00[AMR][1000 genomes]
rs8024131	1.00[EUR][1000 genomes]
rs8035121	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8035295	0.81[YRI][hapmap]
rs8037882	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52595800-52628800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr15:52596200-52623600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:52597800-52629600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:52597800-52643400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr15:52600600-52624200	Weak transcription	Liver	Liver
6	chr15:52600800-52622800	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr15:52600800-52646600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr15:52601000-52622600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:52601000-52643400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr15:52601200-52622600	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr15:52601600-52622400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:52601600-52622800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr15:52601800-52621400	Weak transcription	Psoas Muscle	Psoas
14	chr15:52602000-52622800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:52602200-52622600	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr15:52602600-52622800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr15:52605400-52622800	Strong transcription	HSMMtube	muscle
18	chr15:52607000-52622800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:52607800-52657800	Weak transcription	Small Intestine	intestine
20	chr15:52608600-52622400	Strong transcription	GM12878-XiMat	blood
21	chr15:52608600-52629200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:52609000-52623600	Weak transcription	Hela-S3	cervix
23	chr15:52609800-52622000	Weak transcription	Osteobl	bone
24	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr15:52610000-52643400	Weak transcription	Placenta	Placenta
26	chr15:52611400-52620600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:52611400-52623600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr15:52611400-52629400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr15:52611600-52620800	Weak transcription	Pancreas	Pancrea
30	chr15:52611600-52621000	Weak transcription	Right Atrium	heart
31	chr15:52611600-52621200	Weak transcription	NHDF-Ad	bronchial
32	chr15:52611600-52621600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr15:52611600-52621800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:52611600-52629800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr15:52611600-52650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:52611800-52623600	Weak transcription	A549	lung
37	chr15:52611800-52623800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr15:52611800-52675800	Weak transcription	Gastric	stomach
39	chr15:52613000-52642600	Weak transcription	Colon Smooth Muscle	Colon
40	chr15:52613200-52621200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr15:52613600-52623600	Strong transcription	HUVEC	blood vessel
42	chr15:52613600-52666600	Weak transcription	Right Ventricle	heart
43	chr15:52613800-52623800	Weak transcription	Fetal Heart	heart
44	chr15:52614000-52621400	Weak transcription	Ovary	ovary
45	chr15:52614600-52622000	Weak transcription	Thymus	Thymus
46	chr15:52614800-52620800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr15:52614800-52620800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr15:52614800-52621400	Weak transcription	HSMM	muscle
49	chr15:52614800-52623800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr15:52614800-52623800	Weak transcription	Brain Angular Gyrus	brain

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