Variant report

Variant	rs2690045
Chromosome Location	chr6:25286521-25286522
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	chr6:25277929..25281528-chr6:25281560..25287992,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs16890271	1.00[ASN][1000 genomes]
rs1810471	0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs1815097	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880270	1.00[EUR][1000 genomes]
rs2328862	1.00[EUR][1000 genomes]
rs2690043	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690044	0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690046	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690047	0.84[YRI][hapmap];0.84[AFR][1000 genomes]
rs2690048	0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690049	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690050	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690051	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690052	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690053	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2690055	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2690056	0.84[AFR][1000 genomes]
rs2690057	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2690058	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690062	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2690063	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2690066	0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690069	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690073	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2690075	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2690076	1.00[EUR][1000 genomes]
rs2690102	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690104	1.00[ASN][1000 genomes]
rs2690116	1.00[EUR][1000 genomes]
rs2744252	0.91[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2744253	0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2744255	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744259	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744260	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744262	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2744263	0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744265	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744266	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744270	0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs2744272	1.00[AFR][1000 genomes]
rs2744273	0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs2744274	0.84[AFR][1000 genomes]
rs2744275	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744276	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744277	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744278	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744279	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744280	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744281	0.91[YRI][hapmap]
rs2744282	0.84[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2744283	0.84[AFR][1000 genomes]
rs2744284	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2744285	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744286	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744291	1.00[EUR][1000 genomes]
rs2744292	1.00[EUR][1000 genomes]
rs34935689	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7743997	1.00[ASN][1000 genomes]
rs7767189	1.00[ASN][1000 genomes]
rs940405	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9688905	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25280800-25302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:25281000-25287800	Weak transcription	Small Intestine	intestine
3	chr6:25281200-25288200	Weak transcription	Esophagus	oesophagus
4	chr6:25281200-25290400	Weak transcription	Ovary	ovary
5	chr6:25281200-25290600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:25281200-25293600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:25281200-25296000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:25281400-25287200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:25281400-25288400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:25281400-25290600	Weak transcription	Adipose Nuclei	Adipose
11	chr6:25281400-25292000	Weak transcription	Fetal Lung	lung
12	chr6:25281400-25295800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:25281400-25295800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:25281400-25295800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr6:25281400-25296000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:25281600-25287600	Weak transcription	Stomach Mucosa	stomach
17	chr6:25281600-25287800	Weak transcription	Right Atrium	heart
18	chr6:25281600-25288200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:25281600-25288200	Weak transcription	Fetal Heart	heart
20	chr6:25281600-25288200	Weak transcription	Pancreas	Pancrea
21	chr6:25281600-25290400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:25281600-25290600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:25281600-25290600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:25281600-25293800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:25281600-25293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:25281600-25294400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr6:25281600-25295600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:25281600-25295800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:25281600-25295800	Weak transcription	Thymus	Thymus
30	chr6:25281600-25296000	Weak transcription	Primary T cells from cord blood	blood
31	chr6:25281600-25296000	Weak transcription	Fetal Thymus	thymus
32	chr6:25281600-25296400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:25281800-25288400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr6:25281800-25288400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:25281800-25290600	Weak transcription	Fetal Intestine Large	intestine
36	chr6:25281800-25291600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:25281800-25292400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr6:25281800-25295800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:25282000-25292400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:25282200-25293800	Weak transcription	Lung	lung
41	chr6:25282800-25296400	Weak transcription	Hela-S3	cervix
42	chr6:25283200-25287400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr6:25283400-25287600	Weak transcription	Aorta	Aorta
44	chr6:25283600-25290400	Weak transcription	Left Ventricle	heart
45	chr6:25283800-25288200	Weak transcription	Gastric	stomach
46	chr6:25284600-25286600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:25284600-25290600	Weak transcription	A549	lung
48	chr6:25285000-25286600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:25285200-25288000	Weak transcription	Fetal Intestine Small	intestine
50	chr6:25285400-25286800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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