Variant report

Variant	rs4542605
Chromosome Location	chr15:52339736-52339737
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52309859..52315433-chr15:52338782..52357079,28	MCF-7	breast:
2	chr15:52339219..52341051-chr15:52343518..52345839,3	MCF-7	breast:
3	chr15:52327906..52330801-chr15:52336087..52340276,6	MCF-7	breast:
4	chr15:52339448..52341029-chr15:52351279..52354022,2	MCF-7	breast:
5	chr15:52311160..52314129-chr15:52338657..52341063,3	MCF-7	breast:
6	chr15:52294207..52297195-chr15:52339559..52341402,2	MCF-7	breast:
7	chr15:52332465..52334999-chr15:52337431..52339850,2	K562	blood:

Variant related genes	Relation type
ENSG00000069956	Chromatin interaction
ENSG00000259438	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11070877	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017974	0.89[EUR][1000 genomes]
rs2414127	0.83[ASN][1000 genomes]
rs4627278	0.95[ASN][1000 genomes]
rs7163418	0.90[ASN][1000 genomes]
rs7166425	0.97[ASN][1000 genomes]
rs8034167	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050664	chr15:52265723-52342101	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv530681	chr15:52297253-52390470	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52312800-52345400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:52314400-52359800	Weak transcription	Fetal Brain Male	brain
3	chr15:52325800-52342200	Weak transcription	HUVEC	blood vessel
4	chr15:52326800-52342800	Weak transcription	Fetal Brain Female	brain
5	chr15:52327000-52340600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:52327600-52340200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:52332400-52348200	Weak transcription	Colonic Mucosa	Colon
8	chr15:52332600-52340400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:52332600-52342400	Weak transcription	NHDF-Ad	bronchial
10	chr15:52332600-52349000	Weak transcription	Esophagus	oesophagus
11	chr15:52332600-52349400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:52332600-52350800	Weak transcription	Aorta	Aorta
13	chr15:52332600-52361800	Weak transcription	Gastric	stomach
14	chr15:52332800-52340400	Weak transcription	Brain Germinal Matrix	brain
15	chr15:52332800-52340400	Weak transcription	Placenta	Placenta
16	chr15:52332800-52344400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr15:52333000-52340200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:52333000-52340400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:52333000-52341000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:52333000-52341000	Weak transcription	HSMM	muscle
21	chr15:52333000-52344200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr15:52333000-52344400	Weak transcription	Left Ventricle	heart
23	chr15:52333000-52345400	Weak transcription	Lung	lung
24	chr15:52333000-52348200	Weak transcription	HSMMtube	muscle
25	chr15:52333000-52350800	Weak transcription	Right Ventricle	heart
26	chr15:52333000-52351000	Weak transcription	Spleen	Spleen
27	chr15:52333200-52340800	Weak transcription	Adipose Nuclei	Adipose
28	chr15:52333200-52342800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr15:52333200-52348600	Weak transcription	Colon Smooth Muscle	Colon
30	chr15:52334000-52361400	Weak transcription	Small Intestine	intestine
31	chr15:52334200-52343800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:52334400-52343000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:52334600-52340400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr15:52334600-52344200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr15:52334600-52344200	Weak transcription	Fetal Kidney	kidney
36	chr15:52334600-52357200	Weak transcription	Fetal Heart	heart
37	chr15:52334800-52340200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr15:52334800-52350200	Weak transcription	Psoas Muscle	Psoas
39	chr15:52335000-52340400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:52335000-52344200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr15:52335000-52344200	Weak transcription	Hela-S3	cervix
42	chr15:52335000-52348000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr15:52335400-52341800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:52335400-52344200	Weak transcription	Ovary	ovary
45	chr15:52335400-52350800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr15:52335400-52350800	Weak transcription	Pancreas	Pancrea
47	chr15:52336400-52340800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:52337400-52339800	Enhancers	Brain Anterior Caudate	brain
49	chr15:52337400-52341600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:52337600-52339800	Enhancers	Brain Hippocampus Middle	brain

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