Variant report

Variant	rs55788913
Chromosome Location	chr13:50104249-50104250
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50100974..50104825-chr13:50157801..50160843,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136144	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12428300	0.84[AMR][1000 genomes]
rs12429621	0.84[AMR][1000 genomes]
rs17073175	0.84[AMR][1000 genomes]
rs2296502	0.84[AMR][1000 genomes]
rs60723161	1.00[EUR][1000 genomes]
rs73190749	0.84[AMR][1000 genomes]
rs7994710	1.00[EUR][1000 genomes]
rs7995006	0.84[AMR][1000 genomes]
rs7998078	1.00[EUR][1000 genomes]
rs7998996	1.00[EUR][1000 genomes]
rs9316456	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568239	0.81[AFR][1000 genomes]
rs9596127	1.00[EUR][1000 genomes]
rs9596137	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50075000-50143800	Weak transcription	Small Intestine	intestine
2	chr13:50077600-50114000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr13:50080000-50107000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr13:50080200-50104600	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr13:50080600-50104600	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr13:50084000-50104800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr13:50085400-50104800	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr13:50086400-50113600	Weak transcription	Brain Angular Gyrus	brain
9	chr13:50086600-50106200	Strong transcription	Fetal Thymus	thymus
10	chr13:50086600-50108800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr13:50086600-50114200	Weak transcription	Fetal Brain Female	brain
12	chr13:50088200-50113600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr13:50088400-50151000	Weak transcription	Psoas Muscle	Psoas
14	chr13:50088600-50134200	Weak transcription	Stomach Mucosa	stomach
15	chr13:50089200-50107400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr13:50089400-50114200	Weak transcription	Colon Smooth Muscle	Colon
17	chr13:50090000-50113600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr13:50090000-50122800	Weak transcription	Ovary	ovary
19	chr13:50090000-50123600	Weak transcription	Esophagus	oesophagus
20	chr13:50090200-50114200	Weak transcription	Aorta	Aorta
21	chr13:50090200-50117800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr13:50090400-50106600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr13:50090400-50113400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr13:50090400-50114200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr13:50091000-50114200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr13:50091400-50138800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr13:50091800-50107600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr13:50092000-50108000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr13:50092000-50112200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr13:50092000-50114200	Weak transcription	Fetal Brain Male	brain
31	chr13:50092200-50105400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr13:50092200-50105800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr13:50092200-50113400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr13:50093000-50108000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr13:50093800-50113400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr13:50094000-50112000	Weak transcription	HSMMtube	muscle
37	chr13:50094000-50114200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr13:50094200-50107800	Weak transcription	HepG2	liver
39	chr13:50094600-50113600	Weak transcription	Gastric	stomach
40	chr13:50094600-50113800	Weak transcription	Pancreas	Pancrea
41	chr13:50094600-50120000	Weak transcription	Spleen	Spleen
42	chr13:50094600-50141600	Weak transcription	Right Ventricle	heart
43	chr13:50095000-50120400	Weak transcription	A549	lung
44	chr13:50096000-50108000	Weak transcription	Lung	lung
45	chr13:50096600-50106800	Weak transcription	Fetal Kidney	kidney
46	chr13:50097600-50113600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr13:50097600-50114000	Weak transcription	Fetal Lung	lung
48	chr13:50097800-50105000	Weak transcription	Brain Hippocampus Middle	brain
49	chr13:50097800-50107800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr13:50097800-50113400	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links