Variant report

Variant	rs3130039
Chromosome Location	chr6:30500536-30500537
allele	C/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30451203..30451876-chr6:30500417..30501033,3	MCF-7	breast:
2	chr6:30451171..30452124-chr6:30499936..30500898,4	K562	blood:
3	chr6:30458227..30458900-chr6:30500230..30500946,2	MCF-7	breast:
4	chr6:30464388..30464899-chr6:30500211..30500835,2	MCF-7	breast:
5	chr6:30461707..30464004-chr6:30498859..30501819,2	MCF-7	breast:
6	chr6:30457150..30459406-chr6:30498043..30501943,4	K562	blood:
7	chr6:30455559..30458107-chr6:30499616..30502818,3	MCF-7	breast:
8	chr6:30498128..30503882-chr6:30581008..30585701,7	K562	blood:
9	chr6:30464223..30465018-chr6:30499963..30500762,2	MCF-7	breast:
10	chr6:30498826..30501960-chr6:30560554..30564366,3	MCF-7	breast:
11	chr6:30500351..30502392-chr6:30508622..30511098,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000222894	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000204592	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1058318	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1264432	0.82[EUR][1000 genomes]
rs1264437	0.85[EUR][1000 genomes]
rs1264438	0.85[EUR][1000 genomes]
rs1264439	0.85[EUR][1000 genomes]
rs1264440	0.85[EUR][1000 genomes]
rs1264448	0.83[EUR][1000 genomes]
rs1264456	0.82[EUR][1000 genomes]
rs1362119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468079	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2023608	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2023609	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074503	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2074504	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2074505	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2109477	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2252745	0.81[EUR][1000 genomes]
rs2269709	0.88[EUR][1000 genomes]
rs2269710	0.84[EUR][1000 genomes]
rs2429655	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2429656	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2508021	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2508022	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2508023	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2508024	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2516639	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516641	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2516642	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516643	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516644	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516646	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516647	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2516648	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516649	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516653	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2516655	0.82[EUR][1000 genomes]
rs2516656	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516662	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516665	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2524221	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2524223	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2524224	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2524225	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2524226	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2534802	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2534803	0.84[EUR][1000 genomes]
rs2534804	0.84[EUR][1000 genomes]
rs2534805	0.82[EUR][1000 genomes]
rs2534806	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2534807	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2534808	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2534809	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2534810	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2534811	0.81[AMR][1000 genomes]
rs2534812	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2534813	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2534814	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2534815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2534817	0.84[EUR][1000 genomes]
rs2534820	0.82[EUR][1000 genomes]
rs2534821	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2534823	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2534824	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2534825	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844713	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2844714	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2844715	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2844716	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2844717	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844718	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844720	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844721	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2844722	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2844723	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844724	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844725	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3094718	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095280	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130041	0.88[EUR][1000 genomes]
rs3130043	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3130045	0.88[EUR][1000 genomes]
rs3130240	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3130242	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130243	0.89[EUR][1000 genomes]
rs3130244	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3132609	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3132612	0.85[EUR][1000 genomes]
rs3132613	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132614	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9262070	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9262082	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9262118	0.91[EUR][1000 genomes]
rs975195	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs996588	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs996589	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][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	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
8	nsv884090	chr6:30497652-30510992	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	6 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	chr6:30495000-30501200	Enhancers	Primary B cells from cord blood	blood
2	chr6:30496400-30513400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:30497600-30513400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:30498400-30501400	Weak transcription	Fetal Intestine Large	intestine
5	chr6:30498600-30501400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr6:30498800-30501200	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr6:30499400-30502000	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr6:30499600-30500800	Enhancers	Primary hematopoietic stem cells	blood
9	chr6:30499800-30501800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:30500000-30500600	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr6:30500000-30500600	Enhancers	Right Atrium	heart
12	chr6:30500000-30500600	Enhancers	Thymus	Thymus
13	chr6:30500000-30500800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr6:30500000-30500800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:30500000-30500800	Enhancers	Fetal Thymus	thymus
16	chr6:30500000-30500800	Enhancers	Dnd41	blood
17	chr6:30500000-30501200	Enhancers	HepG2	liver
18	chr6:30500200-30500600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:30500200-30500600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:30500200-30500600	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr6:30500200-30500600	Flanking Active TSS	Brain Angular Gyrus	brain
22	chr6:30500200-30500600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr6:30500200-30500600	Enhancers	HUVEC	blood vessel
24	chr6:30500200-30500800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr6:30500200-30500800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:30500200-30501200	Enhancers	Colonic Mucosa	Colon
27	chr6:30500200-30501800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:30500400-30500600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:30500400-30500600	Active TSS	Liver	Liver
30	chr6:30500400-30500600	Active TSS	Colon Smooth Muscle	Colon
31	chr6:30500400-30500600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr6:30500400-30500800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:30500400-30500800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:30500400-30500800	Flanking Active TSS	Primary B cells from peripheral blood	blood
35	chr6:30500400-30500800	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr6:30500400-30500800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr6:30500400-30500800	Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr6:30500400-30500800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr6:30500400-30500800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:30500400-30500800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr6:30500400-30500800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:30500400-30500800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:30500400-30500800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:30500400-30500800	Active TSS	Brain Hippocampus Middle	brain
45	chr6:30500400-30500800	Active TSS	Duodenum Mucosa	Duodenum
46	chr6:30500400-30500800	Active TSS	Fetal Lung	lung
47	chr6:30500400-30500800	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr6:30500400-30500800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr6:30500400-30500800	Active TSS	Rectal Smooth Muscle	rectum
50	chr6:30500400-30500800	Active TSS	Stomach Smooth Muscle	stomach

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