Variant report

Variant	rs539306
Chromosome Location	chr11:63437787-63437788
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:63437372..63440690-chr11:63447067..63450757,11	K562	blood:
2	chr11:63403442..63405332-chr11:63435637..63437962,2	K562	blood:
3	chr11:63437085..63438927-chr11:63580871..63582709,2	MCF-7	breast:
4	chr11:63436138..63441406-chr11:63446930..63451361,18	MCF-7	breast:
5	chr11:63429933..63433001-chr11:63436097..63439053,5	K562	blood:
6	chr11:63436203..63440489-chr11:63447864..63452214,13	MCF-7	breast:
7	chr11:63437417..63439651-chr11:63532413..63534182,2	MCF-7	breast:
8	chr11:63437085..63438934-chr11:63535581..63537340,2	MCF-7	breast:
9	chr11:63437131..63441413-chr11:63464952..63468959,4	MCF-7	breast:
10	chr11:63437518..63440264-chr11:63931610..63934606,2	MCF-7	breast:
11	chr11:63435682..63438196-chr11:63440536..63442801,2	MCF-7	breast:
12	chr11:63436319..63439202-chr11:63579775..63581446,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000271100	Chromatin interaction
ENSG00000256789	Chromatin interaction
ENSG00000133315	Chromatin interaction
ENSG00000133318	Chromatin interaction
ENSG00000188070	Chromatin interaction
ENSG00000255651	Chromatin interaction
ENSG00000168005	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10501394	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231535	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231543	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11551942	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11551944	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11820129	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1186941	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211688	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12274980	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17158453	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656941	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1789219	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2509744	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959876	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959880	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959881	0.88[EUR][1000 genomes]
rs2959886	0.86[EUR][1000 genomes]
rs3016865	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34109368	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35345497	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35754698	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476034	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476691	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484619	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491231	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500726	0.91[EUR][1000 genomes]
rs500991	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511819	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515645	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517700	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518490	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518692	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521464	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523093	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523809	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534505	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534876	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541809	0.97[EUR][1000 genomes]
rs550629	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551466	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557882	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559405	0.94[EUR][1000 genomes]
rs560938	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566813	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567756	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568769	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568790	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580695	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588523	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928162	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928163	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928165	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928166	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928167	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928168	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928195	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928196	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928197	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928202	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928203	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928204	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928205	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928206	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928208	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928209	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928211	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928212	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928214	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928234	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928236	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928237	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928238	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928239	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928241	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928243	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928244	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928245	0.87[EUR][1000 genomes]
rs61928246	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928247	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61928248	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61929731	0.87[EUR][1000 genomes]
rs6591821	0.89[EUR][1000 genomes]
rs6591822	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106670	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111395	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117206	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7119961	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127454	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128040	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128970	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7928900	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931908	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7932117	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7939940	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943981	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7944003	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7944094	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945972	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949389	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949447	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv832183	chr11:63416678-63564565	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63399800-63437800	Weak transcription	Fetal Brain Female	brain
2	chr11:63411000-63437800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:63423400-63438000	Weak transcription	Fetal Thymus	thymus
4	chr11:63425600-63437800	Weak transcription	Fetal Intestine Small	intestine
5	chr11:63432000-63438200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:63433200-63438200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:63434000-63438000	Enhancers	Small Intestine	intestine
8	chr11:63434600-63437800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr11:63434600-63437800	Enhancers	Left Ventricle	heart
10	chr11:63434600-63438000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr11:63434800-63438000	Enhancers	Primary T cells fromperipheralblood	blood
12	chr11:63434800-63438000	Flanking Active TSS	Hela-S3	cervix
13	chr11:63435000-63437800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr11:63435400-63437800	Enhancers	Colonic Mucosa	Colon
15	chr11:63435600-63438200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr11:63435800-63437800	Weak transcription	Thymus	Thymus
17	chr11:63436200-63437800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr11:63436800-63437800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:63437000-63437800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:63437000-63438000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:63437000-63438800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr11:63437200-63437800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr11:63437200-63437800	Enhancers	Primary hematopoietic stem cells	blood
24	chr11:63437200-63437800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:63437200-63437800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:63437200-63437800	Enhancers	Placenta	Placenta
27	chr11:63437200-63437800	Enhancers	Stomach Mucosa	stomach
28	chr11:63437200-63437800	Flanking Active TSS	NHEK	skin
29	chr11:63437200-63438000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:63437200-63438000	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr11:63437200-63438200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr11:63437200-63439200	Active TSS	NHDF-Ad	bronchial
33	chr11:63437200-63439400	Active TSS	NHLF	lung
34	chr11:63437200-63439600	Active TSS	HSMM	muscle
35	chr11:63437400-63437800	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr11:63437400-63437800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:63437400-63437800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr11:63437400-63437800	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr11:63437400-63437800	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr11:63437400-63437800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr11:63437400-63437800	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr11:63437400-63438000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr11:63437400-63438000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr11:63437400-63438000	Flanking Active TSS	Liver	Liver
45	chr11:63437400-63438000	Enhancers	Fetal Heart	heart
46	chr11:63437400-63438000	Flanking Active TSS	HUVEC	blood vessel
47	chr11:63437400-63438200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr11:63437400-63438200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:63437400-63438200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr11:63437400-63438200	Flanking Active TSS	Dnd41	blood

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