Variant report

Variant	rs2269709
Chromosome Location	chr6:30540890-30540891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:210404553..210406882-chr6:30538400..30541136,2	MCF-7	breast:
2	chr6:30537301..30541414-chr6:30578056..30586798,20	MCF-7	breast:
3	chr6:30455964..30458149-chr6:30539664..30541903,3	MCF-7	breast:
4	chr6:30539536..30541082-chr6:30687683..30690438,2	MCF-7	breast:
5	chr6:30538999..30540963-chr6:30688916..30690569,2	MCF-7	breast:
6	chr6:30482719..30486624-chr6:30535507..30541696,8	K562	blood:
7	chr6:30539567..30541678-chr6:30551647..30554215,2	MCF-7	breast:
8	chr6:30538571..30540910-chr6:30846758..30849178,2	MCF-7	breast:
9	chr6:30538716..30541122-chr6:30550002..30551638,2	MCF-7	breast:
10	chr6:30483910..30486517-chr6:30539369..30541462,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204580	Chromatin interaction
ENSG00000082497	Chromatin interaction
ENSG00000203706	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000204592	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204574	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000216101	Chromatin interaction
ENSG00000235781	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1058318	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1264432	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1264437	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1264438	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1264439	0.87[EUR][1000 genomes]
rs1264440	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1264448	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1362119	0.89[EUR][1000 genomes]
rs1468079	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2023608	0.86[EUR][1000 genomes]
rs2023609	0.86[EUR][1000 genomes]
rs2074503	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2074504	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2074505	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2252745	0.82[EUR][1000 genomes]
rs2269710	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2429655	0.86[EUR][1000 genomes]
rs2508021	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2508024	0.81[EUR][1000 genomes]
rs2516639	0.90[EUR][1000 genomes]
rs2516641	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2516642	0.89[EUR][1000 genomes]
rs2516643	0.89[EUR][1000 genomes]
rs2516644	0.89[EUR][1000 genomes]
rs2516646	0.88[EUR][1000 genomes]
rs2516647	0.85[EUR][1000 genomes]
rs2516648	0.86[EUR][1000 genomes]
rs2516649	0.88[EUR][1000 genomes]
rs2516653	0.80[EUR][1000 genomes]
rs2516656	0.86[EUR][1000 genomes]
rs2516662	0.86[EUR][1000 genomes]
rs2524221	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2524223	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2524224	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2524225	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2524226	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2534802	0.85[EUR][1000 genomes]
rs2534803	0.81[EUR][1000 genomes]
rs2534804	0.81[EUR][1000 genomes]
rs2534805	0.83[EUR][1000 genomes]
rs2534807	0.86[EUR][1000 genomes]
rs2534808	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2534809	0.81[EUR][1000 genomes]
rs2534810	0.85[EUR][1000 genomes]
rs2534812	0.85[EUR][1000 genomes]
rs2534813	0.86[EUR][1000 genomes]
rs2534814	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2534815	0.89[EUR][1000 genomes]
rs2534817	0.81[EUR][1000 genomes]
rs2534821	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2534823	0.87[EUR][1000 genomes]
rs2534824	0.86[EUR][1000 genomes]
rs2534825	0.85[EUR][1000 genomes]
rs2844713	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2844714	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2844715	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2844716	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2844717	0.85[EUR][1000 genomes]
rs2844718	0.85[EUR][1000 genomes]
rs2844720	0.86[EUR][1000 genomes]
rs2844723	0.87[EUR][1000 genomes]
rs2844724	0.86[EUR][1000 genomes]
rs2844725	0.80[EUR][1000 genomes]
rs3094718	0.89[EUR][1000 genomes]
rs3130039	0.88[EUR][1000 genomes]
rs3130041	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3130043	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3130045	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3130240	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3130242	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130243	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130244	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3132609	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132612	0.86[EUR][1000 genomes]
rs3132613	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3132614	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9262070	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9262082	0.86[EUR][1000 genomes]
rs9262118	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs975195	0.86[EUR][1000 genomes]
rs996588	0.85[EUR][1000 genomes]
rs996589	0.84[EUR][1000 genomes]

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	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
5	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
6	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
7	nsv884091	chr6:30526026-30590646	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	776 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30539800-30541000	Enhancers	Gastric	stomach
2	chr6:30539800-30541000	Flanking Active TSS	HepG2	liver
3	chr6:30539800-30541000	Flanking Active TSS	NHLF	lung
4	chr6:30539800-30541200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:30539800-30541200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:30539800-30541600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:30539800-30541600	Enhancers	Small Intestine	intestine
8	chr6:30539800-30541600	Enhancers	Spleen	Spleen
9	chr6:30540000-30541000	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr6:30540000-30541000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:30540000-30541000	Flanking Active TSS	Fetal Intestine Small	intestine
12	chr6:30540000-30541000	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr6:30540000-30541200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:30540000-30541200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:30540000-30541200	Enhancers	Placenta Amnion	Placenta Amnion
16	chr6:30540000-30541800	Transcr. at gene 5' and 3'	Dnd41	blood
17	chr6:30540000-30541800	Flanking Active TSS	GM12878-XiMat	blood
18	chr6:30540000-30541800	Transcr. at gene 5' and 3'	K562	blood
19	chr6:30540000-30542000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:30540000-30544400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:30540000-30544400	Weak transcription	Ovary	ovary
22	chr6:30540000-30545400	Weak transcription	Aorta	Aorta
23	chr6:30540200-30541000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:30540200-30541000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:30540200-30541000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:30540200-30541000	Enhancers	Brain Cingulate Gyrus	brain
27	chr6:30540200-30541000	Enhancers	Brain Hippocampus Middle	brain
28	chr6:30540200-30541000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr6:30540200-30541000	Enhancers	Fetal Brain Male	brain
30	chr6:30540200-30541000	Enhancers	Fetal Muscle Leg	muscle
31	chr6:30540200-30541000	Enhancers	Placenta	Placenta
32	chr6:30540200-30541000	Enhancers	Pancreas	Pancrea
33	chr6:30540200-30541000	Enhancers	Psoas Muscle	Psoas
34	chr6:30540200-30541200	Enhancers	Primary B cells from peripheral blood	blood
35	chr6:30540200-30541200	Enhancers	Brain Angular Gyrus	brain
36	chr6:30540200-30541200	Enhancers	Brain Anterior Caudate	brain
37	chr6:30540200-30541200	Enhancers	Esophagus	oesophagus
38	chr6:30540200-30541200	Genic enhancers	Fetal Stomach	stomach
39	chr6:30540200-30541200	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr6:30540200-30541200	Enhancers	Rectal Smooth Muscle	rectum
41	chr6:30540200-30541400	Enhancers	Primary B cells from cord blood	blood
42	chr6:30540200-30541400	Enhancers	Fetal Brain Female	brain
43	chr6:30540200-30541600	Enhancers	Primary hematopoietic stem cells	blood
44	chr6:30540200-30541600	Enhancers	Right Ventricle	heart
45	chr6:30540200-30541600	Enhancers	Osteobl	bone
46	chr6:30540200-30542200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:30540200-30542200	Enhancers	Primary T cells fromperipheralblood	blood
48	chr6:30540200-30542200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:30540200-30542200	Enhancers	Right Atrium	heart
50	chr6:30540200-30542400	Enhancers	Pancreatic Islets	Pancreatic Islet

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