Variant report

Variant	rs1620509
Chromosome Location	chr4:57946388-57946389
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57944252..57946823-chr4:57975911..57977962,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245067	Chromatin interaction
ENSG00000163453	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10009533	0.82[CEU][hapmap]
rs10015212	0.95[ASN][1000 genomes]
rs10019698	0.85[ASN][1000 genomes]
rs11722333	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1522609	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1713976	0.82[CEU][hapmap]
rs1713979	0.82[CEU][hapmap]
rs1714004	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1714005	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1714006	0.95[ASN][1000 genomes]
rs1714007	0.95[ASN][1000 genomes]
rs1714008	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1714009	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718829	0.95[ASN][1000 genomes]
rs1718858	0.95[ASN][1000 genomes]
rs1718859	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718861	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242004	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6827171	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57932400-57947600	Genic enhancers	Osteobl	bone
2	chr4:57934400-57951600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:57934600-57948200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:57935800-57948000	Weak transcription	Fetal Muscle Leg	muscle
5	chr4:57937400-57948000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:57937800-57946800	Weak transcription	Adipose Nuclei	Adipose
7	chr4:57938000-57955800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr4:57938800-57947000	Weak transcription	Esophagus	oesophagus
9	chr4:57939800-57949800	Enhancers	HMEC	breast
10	chr4:57941400-57947000	Weak transcription	Brain Substantia Nigra	brain
11	chr4:57942000-57947000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:57942000-57947800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:57942200-57946600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:57942800-57947000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:57942800-57947000	Enhancers	HUVEC	blood vessel
16	chr4:57942800-57960400	Weak transcription	Psoas Muscle	Psoas
17	chr4:57943200-57950000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:57943800-57946800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:57943800-57948600	Enhancers	HSMM	muscle
20	chr4:57943800-57950200	Enhancers	NHLF	lung
21	chr4:57944000-57947000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr4:57944000-57947000	Genic enhancers	HSMMtube	muscle
23	chr4:57944000-57948200	Enhancers	Fetal Lung	lung
24	chr4:57944000-57948400	Enhancers	Fetal Stomach	stomach
25	chr4:57944400-57946400	Enhancers	Fetal Intestine Small	intestine
26	chr4:57944400-57964000	Weak transcription	Fetal Thymus	thymus
27	chr4:57944600-57947400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr4:57944800-57946400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:57944800-57947800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:57944800-57950000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:57945000-57946400	Enhancers	Brain Anterior Caudate	brain
32	chr4:57945000-57946600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:57945000-57946600	Enhancers	Small Intestine	intestine
34	chr4:57945000-57946800	Enhancers	Muscle Satellite Cultured Cells	--
35	chr4:57945000-57947000	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr4:57945000-57948200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:57945000-57950000	Enhancers	NHDF-Ad	bronchial
38	chr4:57945200-57946800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:57945200-57946800	Weak transcription	Ovary	ovary
40	chr4:57945200-57947200	Enhancers	Aorta	Aorta
41	chr4:57945200-57958000	Weak transcription	Gastric	stomach
42	chr4:57945200-57960400	Weak transcription	Pancreas	Pancrea
43	chr4:57945400-57947000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr4:57945400-57948200	Enhancers	Fetal Heart	heart
45	chr4:57945400-57948400	Enhancers	HepG2	liver
46	chr4:57945400-57948600	Enhancers	Brain Hippocampus Middle	brain
47	chr4:57945400-57948800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:57945400-57950000	Enhancers	NHEK	skin
49	chr4:57945600-57946400	Enhancers	Primary hematopoietic stem cells	blood
50	chr4:57945600-57946600	Enhancers	NH-A	brain

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