Variant report

Variant	rs553941644
Chromosome Location	chr13:52742003-52742004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45194788..45196878-chr13:52740302..52742412,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200169	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

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	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv1037567	chr13:52643647-52802799	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	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
7	nsv976116	chr13:52741751-52768674	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52733800-52743000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:52733800-52757000	Weak transcription	Spleen	Spleen
3	chr13:52734000-52760000	Weak transcription	Gastric	stomach
4	chr13:52734200-52742200	Weak transcription	Fetal Lung	lung
5	chr13:52734200-52742400	Weak transcription	Brain Germinal Matrix	brain
6	chr13:52734200-52742400	Weak transcription	Fetal Brain Female	brain
7	chr13:52734200-52742600	Weak transcription	Esophagus	oesophagus
8	chr13:52734200-52743000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr13:52734200-52747800	Weak transcription	Fetal Brain Male	brain
10	chr13:52734200-52751800	Weak transcription	Psoas Muscle	Psoas
11	chr13:52734200-52752400	Weak transcription	GM12878-XiMat	blood
12	chr13:52734200-52754000	Weak transcription	Right Ventricle	heart
13	chr13:52734200-52754000	Weak transcription	Hela-S3	cervix
14	chr13:52734400-52742400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr13:52734400-52742400	Weak transcription	Pancreas	Pancrea
16	chr13:52734400-52746000	Weak transcription	Primary B cells from cord blood	blood
17	chr13:52734400-52746200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr13:52734400-52751200	Weak transcription	Colon Smooth Muscle	Colon
19	chr13:52734400-52753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr13:52734400-52753600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr13:52734400-52754000	Weak transcription	NHEK	skin
22	chr13:52734400-52761000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr13:52734400-52768000	Weak transcription	Aorta	Aorta
24	chr13:52734600-52742800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr13:52734600-52766000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr13:52734800-52742400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr13:52734800-52742400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr13:52735000-52743000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr13:52735000-52744200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr13:52735000-52746200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr13:52735200-52747400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr13:52735400-52742400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr13:52735400-52744000	Weak transcription	Fetal Kidney	kidney
34	chr13:52735600-52754000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr13:52736400-52754000	Weak transcription	Colonic Mucosa	Colon
36	chr13:52736400-52767200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr13:52736600-52742400	Weak transcription	Small Intestine	intestine
38	chr13:52736600-52742600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr13:52736600-52754200	Weak transcription	Fetal Heart	heart
40	chr13:52736800-52742200	Weak transcription	Adipose Nuclei	Adipose
41	chr13:52736800-52765600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr13:52737200-52742400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr13:52737200-52747600	Weak transcription	HSMMtube	muscle
44	chr13:52737200-52748800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr13:52737200-52767400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr13:52737400-52751400	Weak transcription	A549	lung
47	chr13:52737400-52754000	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr13:52737600-52743000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr13:52737800-52742200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr13:52737800-52742800	Weak transcription	Duodenum Mucosa	Duodenum

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