Variant report

Variant	rs2744272
Chromosome Location	chr6:25281599-25281600
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25281539..25283439-chr6:25288987..25290697,2	K562	blood:
2	chr6:25277929..25281528-chr6:25281560..25287992,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs17677216	0.81[EUR][1000 genomes]
rs1810471	0.82[AFR][1000 genomes]
rs1815097	0.84[AFR][1000 genomes]
rs2690043	1.00[AFR][1000 genomes]
rs2690044	1.00[AFR][1000 genomes]
rs2690045	1.00[AFR][1000 genomes]
rs2690046	1.00[AFR][1000 genomes]
rs2690047	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690048	1.00[AFR][1000 genomes]
rs2690049	1.00[AFR][1000 genomes]
rs2690050	1.00[AFR][1000 genomes]
rs2690051	1.00[AFR][1000 genomes]
rs2690052	1.00[AFR][1000 genomes]
rs2690053	0.90[AFR][1000 genomes]
rs2690055	0.89[AFR][1000 genomes]
rs2690056	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690057	0.91[AFR][1000 genomes]
rs2690058	0.87[AFR][1000 genomes]
rs2690062	0.84[AFR][1000 genomes]
rs2690063	0.84[AFR][1000 genomes]
rs2690066	0.84[AFR][1000 genomes]
rs2690069	0.81[AFR][1000 genomes]
rs2690102	0.87[AFR][1000 genomes]
rs2744253	0.81[AFR][1000 genomes]
rs2744255	0.81[AFR][1000 genomes]
rs2744259	0.82[AFR][1000 genomes]
rs2744263	0.87[AFR][1000 genomes]
rs2744265	0.85[AFR][1000 genomes]
rs2744266	0.87[AFR][1000 genomes]
rs2744270	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744273	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744274	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744275	1.00[AFR][1000 genomes]
rs2744276	1.00[AFR][1000 genomes]
rs2744277	1.00[AFR][1000 genomes]
rs2744278	1.00[AFR][1000 genomes]
rs2744279	1.00[AFR][1000 genomes]
rs2744280	1.00[AFR][1000 genomes]
rs2744282	0.84[AFR][1000 genomes]
rs2744283	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744284	1.00[AFR][1000 genomes]
rs2744285	1.00[AFR][1000 genomes]
rs2744286	1.00[AFR][1000 genomes]
rs6939174	0.81[EUR][1000 genomes]
rs940405	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv883484	chr6:25237288-25303100	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25278400-25281600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:25278400-25281600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:25278400-25281600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr6:25278600-25283400	Active TSS	Aorta	Aorta
5	chr6:25278800-25281600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:25278800-25281600	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr6:25278800-25281600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:25278800-25281600	Active TSS	Right Atrium	heart
9	chr6:25279000-25281600	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:25279000-25281600	Active TSS	Left Ventricle	heart
11	chr6:25279000-25281800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:25279000-25281800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:25279000-25281800	Active TSS	Fetal Intestine Large	intestine
14	chr6:25279200-25281600	Active TSS	Brain Cingulate Gyrus	brain
15	chr6:25279200-25281600	Active TSS	NHLF	lung
16	chr6:25279200-25281800	Active TSS	Brain Angular Gyrus	brain
17	chr6:25280000-25281600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:25280600-25281600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:25280600-25281600	Active TSS	Rectal Smooth Muscle	rectum
20	chr6:25280600-25281600	Flanking Active TSS	HMEC	breast
21	chr6:25280800-25281600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr6:25280800-25281600	Enhancers	Primary T cells fromperipheralblood	blood
23	chr6:25280800-25281800	Flanking Active TSS	NHEK	skin
24	chr6:25280800-25302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:25281000-25281600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr6:25281000-25281600	Enhancers	Fetal Heart	heart
27	chr6:25281000-25281600	Enhancers	Placenta	Placenta
28	chr6:25281000-25281600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr6:25281000-25281600	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr6:25281000-25281600	Enhancers	HepG2	liver
31	chr6:25281000-25281800	Active TSS	Duodenum Mucosa	Duodenum
32	chr6:25281000-25286000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr6:25281000-25287800	Weak transcription	Small Intestine	intestine
34	chr6:25281200-25281600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:25281200-25281600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:25281200-25281600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:25281200-25281600	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr6:25281200-25281600	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr6:25281200-25281600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:25281200-25281600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:25281200-25281600	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr6:25281200-25281600	Enhancers	Primary T cells from cord blood	blood
43	chr6:25281200-25281600	Enhancers	Primary hematopoietic stem cells	blood
44	chr6:25281200-25281600	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr6:25281200-25281600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:25281200-25281600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:25281200-25281600	Active TSS	Brain Anterior Caudate	brain
48	chr6:25281200-25281600	Enhancers	Colonic Mucosa	Colon
49	chr6:25281200-25281600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
50	chr6:25281200-25281600	Enhancers	Fetal Thymus	thymus

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