Variant report

Variant	rs6769720
Chromosome Location	chr3:52764350-52764351
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr3:52764183-52764360	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52738889..52741112-chr3:52764320..52766937,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270941	TF binding region
ENSG00000016864	Chromatin interaction
ENSG00000114902	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11510435	1.00[EUR][1000 genomes]
rs12107484	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17052357	1.00[EUR][1000 genomes]
rs17052404	1.00[EUR][1000 genomes]
rs34173244	1.00[EUR][1000 genomes]
rs4532127	1.00[EUR][1000 genomes]
rs56134416	1.00[EUR][1000 genomes]
rs56156188	1.00[EUR][1000 genomes]
rs56276589	1.00[EUR][1000 genomes]
rs56665533	1.00[EUR][1000 genomes]
rs57008939	1.00[EUR][1000 genomes]
rs57298447	1.00[EUR][1000 genomes]
rs57757646	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57789542	1.00[EUR][1000 genomes]
rs57869735	1.00[EUR][1000 genomes]
rs57946083	1.00[EUR][1000 genomes]
rs58409398	1.00[EUR][1000 genomes]
rs58528592	1.00[EUR][1000 genomes]
rs58564212	1.00[EUR][1000 genomes]
rs59638016	1.00[EUR][1000 genomes]
rs59869286	1.00[EUR][1000 genomes]
rs60040519	1.00[EUR][1000 genomes]
rs60058353	1.00[EUR][1000 genomes]
rs60256157	1.00[EUR][1000 genomes]
rs60311166	1.00[EUR][1000 genomes]
rs60770874	1.00[EUR][1000 genomes]
rs60830326	1.00[EUR][1000 genomes]
rs61220667	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61538294	1.00[EUR][1000 genomes]
rs6445536	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6762788	1.00[EUR][1000 genomes]
rs6780005	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6780397	1.00[EUR][1000 genomes]
rs72950424	1.00[EUR][1000 genomes]
rs72950432	1.00[EUR][1000 genomes]
rs72950437	1.00[EUR][1000 genomes]
rs72960212	1.00[EUR][1000 genomes]
rs72960237	1.00[EUR][1000 genomes]
rs72960240	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960260	1.00[EUR][1000 genomes]
rs72960274	1.00[EUR][1000 genomes]
rs72960281	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960285	1.00[EUR][1000 genomes]
rs72965177	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72965181	1.00[EUR][1000 genomes]
rs73839126	1.00[EUR][1000 genomes]
rs73839129	1.00[EUR][1000 genomes]
rs7619643	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7645785	1.00[EUR][1000 genomes]
rs764636	1.00[EUR][1000 genomes]
rs7647992	1.00[EUR][1000 genomes]
rs934839	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv508219	chr3:52741193-52803899	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52741400-52765600	Weak transcription	Aorta	Aorta
2	chr3:52741400-52766600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:52741600-52765600	Weak transcription	Esophagus	oesophagus
4	chr3:52741600-52804000	Weak transcription	Psoas Muscle	Psoas
5	chr3:52742000-52765600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:52742000-52766400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:52742000-52766400	Weak transcription	NHLF	lung
8	chr3:52742000-52766600	Weak transcription	Hela-S3	cervix
9	chr3:52742000-52766600	Weak transcription	NHEK	skin
10	chr3:52742200-52767200	Weak transcription	Fetal Brain Male	brain
11	chr3:52742200-52768800	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:52742400-52771400	Weak transcription	K562	blood
13	chr3:52742400-52772800	Weak transcription	Pancreas	Pancrea
14	chr3:52742600-52766000	Weak transcription	HUVEC	blood vessel
15	chr3:52743000-52766600	Weak transcription	NH-A	brain
16	chr3:52743000-52766600	Weak transcription	NHDF-Ad	bronchial
17	chr3:52743200-52766600	Weak transcription	Osteobl	bone
18	chr3:52744000-52765400	Weak transcription	HMEC	breast
19	chr3:52744800-52767000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:52746800-52764400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:52747000-52765400	Weak transcription	Spleen	Spleen
22	chr3:52747000-52765600	Weak transcription	Brain Anterior Caudate	brain
23	chr3:52747000-52766600	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:52749000-52764800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:52749000-52771600	Weak transcription	Colonic Mucosa	Colon
26	chr3:52749200-52764400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:52749200-52766800	Weak transcription	Right Ventricle	heart
28	chr3:52749200-52767000	Weak transcription	Fetal Heart	heart
29	chr3:52749200-52767400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:52749200-52779800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:52749400-52766600	Weak transcription	Gastric	stomach
32	chr3:52749400-52776200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:52750000-52765600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:52750000-52765600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:52750200-52765400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:52753400-52765400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:52753400-52765600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:52753400-52765600	Weak transcription	Brain Substantia Nigra	brain
39	chr3:52753400-52765600	Weak transcription	Ovary	ovary
40	chr3:52753600-52765400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:52754200-52766200	Weak transcription	Brain Germinal Matrix	brain
42	chr3:52755400-52764400	Weak transcription	Brain Angular Gyrus	brain
43	chr3:52755800-52765600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:52755800-52767200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:52756200-52764400	Weak transcription	Primary T cells from cord blood	blood
46	chr3:52756200-52767400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:52756200-52777400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:52756400-52765800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:52756600-52764800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:52756600-52767200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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