Variant report

Variant	rs2690056
Chromosome Location	chr6:25281848-25281849
allele	C/G
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]
rs12203442	1.00[CHB][hapmap]
rs17677216	0.81[EUR][1000 genomes]
rs1810471	1.00[CHB][hapmap]
rs2690043	0.84[AFR][1000 genomes]
rs2690044	0.83[YRI][hapmap];0.84[AFR][1000 genomes]
rs2690045	0.84[AFR][1000 genomes]
rs2690046	0.84[AFR][1000 genomes]
rs2690047	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690048	0.84[AFR][1000 genomes]
rs2690049	0.84[AFR][1000 genomes]
rs2690050	0.84[AFR][1000 genomes]
rs2690051	0.84[AFR][1000 genomes]
rs2690052	0.84[AFR][1000 genomes]
rs2690062	1.00[CHB][hapmap]
rs2690066	1.00[CHB][hapmap]
rs2744263	1.00[CHB][hapmap]
rs2744270	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744272	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744275	0.84[AFR][1000 genomes]
rs2744276	0.84[AFR][1000 genomes]
rs2744277	0.84[AFR][1000 genomes]
rs2744278	0.83[YRI][hapmap];0.84[AFR][1000 genomes]
rs2744279	1.00[CHB][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes]
rs2744280	0.84[AFR][1000 genomes]
rs2744281	1.00[CHB][hapmap]
rs2744282	0.94[YRI][hapmap];1.00[AFR][1000 genomes]
rs2744283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744284	0.84[AFR][1000 genomes]
rs2744285	0.84[AFR][1000 genomes]
rs2744286	1.00[CHB][hapmap];0.84[AFR][1000 genomes]
rs303005	1.00[CHB][hapmap]
rs4594940	1.00[CHB][hapmap]
rs6456661	1.00[CHB][hapmap]
rs6913606	1.00[CEU][hapmap]
rs6913886	1.00[CEU][hapmap]
rs6936496	1.00[CEU][hapmap]
rs6939174	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7743508	1.00[CHB][hapmap]
rs7743997	1.00[CHB][hapmap]
rs7755701	1.00[CEU][hapmap]
rs7756143	1.00[CEU][hapmap]
rs9358852	1.00[CEU][hapmap]
rs9366616	1.00[CEU][hapmap]

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:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25278600-25283400	Active TSS	Aorta	Aorta
2	chr6:25280800-25302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:25281000-25286000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr6:25281000-25287800	Weak transcription	Small Intestine	intestine
5	chr6:25281200-25288200	Weak transcription	Esophagus	oesophagus
6	chr6:25281200-25290400	Weak transcription	Ovary	ovary
7	chr6:25281200-25290600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:25281200-25293600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:25281200-25296000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:25281400-25286200	Weak transcription	Liver	Liver
11	chr6:25281400-25286400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:25281400-25287200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:25281400-25288400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:25281400-25290600	Weak transcription	Adipose Nuclei	Adipose
15	chr6:25281400-25292000	Weak transcription	Fetal Lung	lung
16	chr6:25281400-25295800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:25281400-25295800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:25281400-25295800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:25281400-25296000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:25281600-25282000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr6:25281600-25282600	Weak transcription	Hela-S3	cervix
22	chr6:25281600-25283400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:25281600-25283400	Weak transcription	Gastric	stomach
24	chr6:25281600-25283400	Weak transcription	A549	lung
25	chr6:25281600-25283600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:25281600-25283600	Weak transcription	HMEC	breast
27	chr6:25281600-25283800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:25281600-25284800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:25281600-25285800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:25281600-25285800	Weak transcription	HepG2	liver
31	chr6:25281600-25286200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:25281600-25287600	Weak transcription	Stomach Mucosa	stomach
33	chr6:25281600-25287800	Weak transcription	Right Atrium	heart
34	chr6:25281600-25288200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr6:25281600-25288200	Weak transcription	Fetal Heart	heart
36	chr6:25281600-25288200	Weak transcription	Pancreas	Pancrea
37	chr6:25281600-25290400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:25281600-25290600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:25281600-25290600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:25281600-25293800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:25281600-25293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:25281600-25294400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr6:25281600-25295600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr6:25281600-25295800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:25281600-25295800	Weak transcription	Thymus	Thymus
46	chr6:25281600-25296000	Weak transcription	Primary T cells from cord blood	blood
47	chr6:25281600-25296000	Weak transcription	Fetal Thymus	thymus
48	chr6:25281600-25296400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:25281800-25282000	Weak transcription	Lung	lung
50	chr6:25281800-25282400	Weak transcription	Duodenum Mucosa	Duodenum

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