Variant report

Variant	rs7623477
Chromosome Location	chr3:143568158-143568159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143566553..143569042-chr3:143690803..143692633,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10433436	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11714060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1319100	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1319101	1.00[EUR][1000 genomes]
rs1394398	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1394402	1.00[EUR][1000 genomes]
rs1979911	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1995529	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1995530	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2011290	1.00[EUR][1000 genomes]
rs2361202	1.00[EUR][1000 genomes]
rs2361203	0.94[EUR][1000 genomes]
rs2361205	0.94[EUR][1000 genomes]
rs2361206	0.94[EUR][1000 genomes]
rs2361207	0.94[EUR][1000 genomes]
rs2361208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2361209	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2885193	0.94[EUR][1000 genomes]
rs2885194	0.94[EUR][1000 genomes]
rs2885195	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4286430	0.89[EUR][1000 genomes]
rs4499594	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4839612	0.94[EUR][1000 genomes]
rs4839671	0.94[EUR][1000 genomes]
rs4839672	0.94[EUR][1000 genomes]
rs4839673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440196	0.94[EUR][1000 genomes]
rs6768702	1.00[EUR][1000 genomes]
rs6780027	1.00[EUR][1000 genomes]
rs7627020	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9289669	1.00[EUR][1000 genomes]
rs9824974	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9836851	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9870661	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143565800-143569200	Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr3:143566000-143568200	Active TSS	Brain Anterior Caudate	brain
3	chr3:143566000-143568400	Active TSS	Ovary	ovary
4	chr3:143566200-143568600	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr3:143567400-143568200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:143567400-143568200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr3:143567400-143568400	Enhancers	Fetal Thymus	thymus
8	chr3:143567400-143568800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:143567400-143569000	Enhancers	HSMM	muscle
10	chr3:143567400-143569000	Enhancers	NHEK	skin
11	chr3:143567400-143570000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr3:143567400-143570600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:143567400-143571000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:143567600-143568200	Enhancers	Primary B cells from cord blood	blood
15	chr3:143567600-143568400	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr3:143567600-143568400	Flanking Active TSS	Brain Substantia Nigra	brain
17	chr3:143567600-143569000	Enhancers	HMEC	breast
18	chr3:143567600-143569200	Enhancers	Fetal Stomach	stomach
19	chr3:143567600-143569200	Enhancers	HUVEC	blood vessel
20	chr3:143567600-143569400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr3:143567600-143569600	Enhancers	Primary T cells from cord blood	blood
22	chr3:143567600-143569600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:143567600-143569600	Enhancers	HSMMtube	muscle
24	chr3:143567800-143568200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:143567800-143568200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr3:143567800-143568200	Enhancers	Dnd41	blood
27	chr3:143567800-143568400	Enhancers	Adipose Nuclei	Adipose
28	chr3:143567800-143568600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:143567800-143568600	Enhancers	Muscle Satellite Cultured Cells	--
30	chr3:143567800-143568600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:143567800-143568600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:143567800-143568600	Weak transcription	Fetal Lung	lung
33	chr3:143567800-143568600	Weak transcription	Osteobl	bone
34	chr3:143567800-143568800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:143567800-143568800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:143567800-143568800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:143567800-143568800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:143567800-143569000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:143567800-143569000	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr3:143567800-143569000	Enhancers	NHLF	lung
41	chr3:143567800-143569200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr3:143567800-143569200	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr3:143567800-143569200	Enhancers	NH-A	brain
44	chr3:143567800-143569400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr3:143567800-143569600	Enhancers	Primary T cells fromperipheralblood	blood
46	chr3:143567800-143569600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:143567800-143569600	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr3:143567800-143569600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr3:143567800-143569600	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr3:143567800-143569800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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