Variant report

Variant	rs2534825
Chromosome Location	chr6:30495743-30495744
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30456435..30458673-chr6:30494431..30497074,2	MCF-7	breast:
2	chr6:30455644..30457462-chr6:30495249..30496782,2	K562	blood:
3	chr6:30495618..30498442-chr6:30501086..30503678,2	MCF-7	breast:
4	chr6:30494697..30497060-chr6:30502191..30504973,2	K562	blood:
5	chr6:30494651..30496200-chr6:30498206..30500229,2	K562	blood:
6	chr6:30483372..30485583-chr6:30493790..30495763,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235781	Chromatin interaction
ENSG00000204592	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1058318	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1264437	0.82[EUR][1000 genomes]
rs1264438	0.83[EUR][1000 genomes]
rs1264439	0.82[EUR][1000 genomes]
rs1264440	0.83[EUR][1000 genomes]
rs1264448	0.80[EUR][1000 genomes]
rs1264456	0.83[EUR][1000 genomes]
rs1362119	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1468079	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2023608	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2023609	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074503	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2074504	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2074505	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2109477	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2269709	0.85[EUR][1000 genomes]
rs2269710	0.82[EUR][1000 genomes]
rs2429655	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2429656	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2508021	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2508022	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2508023	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2508024	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2516639	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2516641	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2516642	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2516643	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516644	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516646	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516647	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2516648	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516649	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516653	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516655	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2516656	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516662	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516665	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2524221	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2524223	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2524224	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2524225	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2524226	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2534802	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2534803	0.85[EUR][1000 genomes]
rs2534804	0.85[EUR][1000 genomes]
rs2534805	0.83[EUR][1000 genomes]
rs2534806	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2534807	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2534808	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2534809	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2534810	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2534811	0.82[AMR][1000 genomes]
rs2534812	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2534813	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2534814	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2534815	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2534817	0.85[EUR][1000 genomes]
rs2534820	0.83[EUR][1000 genomes]
rs2534821	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2534823	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2534824	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844713	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2844714	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2844715	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2844716	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2844717	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844718	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844720	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844721	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2844722	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2844723	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844724	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844725	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3094718	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3095280	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3130039	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130041	0.85[EUR][1000 genomes]
rs3130043	0.87[EUR][1000 genomes]
rs3130045	0.85[EUR][1000 genomes]
rs3130240	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130242	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130243	0.86[EUR][1000 genomes]
rs3130244	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3132609	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3132612	0.83[EUR][1000 genomes]
rs3132613	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3132614	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9262070	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9262082	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9262118	0.88[EUR][1000 genomes]
rs975195	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs996588	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs996589	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][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	nsv884077	chr6:30434900-30512163	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	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
7	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

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30486000-30500000	Weak transcription	Thymus	Thymus
2	chr6:30488400-30495800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:30489400-30495800	Weak transcription	Osteobl	bone
4	chr6:30494800-30496600	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr6:30495000-30495800	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:30495000-30495800	Enhancers	HUVEC	blood vessel
7	chr6:30495000-30498800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr6:30495000-30499000	Enhancers	Primary B cells from peripheral blood	blood
9	chr6:30495000-30501200	Enhancers	Primary B cells from cord blood	blood
10	chr6:30495200-30495800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:30495200-30495800	Enhancers	GM12878-XiMat	blood
12	chr6:30495200-30495800	Enhancers	NH-A	brain
13	chr6:30495200-30496000	Active TSS	Duodenum Mucosa	Duodenum
14	chr6:30495200-30496000	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr6:30495200-30496200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:30495200-30498400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr6:30495200-30498400	Enhancers	Fetal Intestine Large	intestine
18	chr6:30495200-30498600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:30495200-30498600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:30495200-30498600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:30495200-30498800	Enhancers	HepG2	liver
22	chr6:30495400-30495800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:30495400-30495800	Active TSS	Muscle Satellite Cultured Cells	--
24	chr6:30495400-30495800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:30495400-30495800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:30495400-30495800	Enhancers	Fetal Muscle Trunk	muscle
27	chr6:30495400-30496200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:30495400-30496200	Enhancers	HSMMtube	muscle
29	chr6:30495400-30496400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:30495400-30496400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:30495400-30496400	Enhancers	Fetal Intestine Small	intestine
32	chr6:30495400-30496400	Enhancers	HMEC	breast
33	chr6:30495400-30498000	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr6:30495400-30498400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr6:30495400-30498600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:30495400-30498800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:30495400-30499000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr6:30495600-30495800	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr6:30495600-30495800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:30495600-30495800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr6:30495600-30495800	Active TSS	A549	lung
42	chr6:30495600-30495800	Enhancers	Hela-S3	cervix
43	chr6:30495600-30495800	Enhancers	NHEK	skin
44	chr6:30495600-30496000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr6:30495600-30496200	Weak transcription	Stomach Mucosa	stomach
46	chr6:30495600-30498200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr6:30495600-30498400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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