Variant report

Variant	rs56004462
Chromosome Location	chr4:15498717-15498718
allele	A/C
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	SETDB1	chr4:15498694-15499049	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15497693..15500487-chr4:15654286..15657058,2	MCF-7	breast:
2	chr4:15493173..15496394-chr4:15497491..15500995,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249930	TF binding region
ENSG00000249930	Chromatin interaction
ENSG00000118564	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1154577	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13131119	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34036638	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35724720	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36012186	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57275698	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6825815	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6835038	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844141	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237149	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73237151	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers 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	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15481600-15519000	Weak transcription	Gastric	stomach
2	chr4:15482200-15519800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:15482600-15516600	Weak transcription	Brain Angular Gyrus	brain
4	chr4:15482600-15526400	Weak transcription	HMEC	breast
5	chr4:15482800-15518200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:15485000-15504800	Weak transcription	Ovary	ovary
7	chr4:15486600-15499800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:15487200-15498800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:15487400-15570400	Weak transcription	Psoas Muscle	Psoas
10	chr4:15490400-15498800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:15490400-15519400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:15490400-15539600	Weak transcription	Esophagus	oesophagus
13	chr4:15490600-15502400	Weak transcription	Lung	lung
14	chr4:15490600-15505000	Weak transcription	Adipose Nuclei	Adipose
15	chr4:15490600-15505200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:15490600-15510600	Weak transcription	Aorta	Aorta
17	chr4:15490600-15519000	Weak transcription	A549	lung
18	chr4:15490800-15504600	Weak transcription	Fetal Kidney	kidney
19	chr4:15491000-15504400	Weak transcription	Fetal Intestine Large	intestine
20	chr4:15491200-15504800	Weak transcription	Osteobl	bone
21	chr4:15491600-15498800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:15491600-15502400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:15491600-15504400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr4:15491600-15511400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:15491800-15516400	Weak transcription	NHLF	lung
26	chr4:15492200-15503600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:15492200-15511000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr4:15492400-15505000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:15492400-15505200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:15493400-15504400	Weak transcription	Fetal Intestine Small	intestine
31	chr4:15493400-15504800	Weak transcription	Left Ventricle	heart
32	chr4:15495600-15559400	Weak transcription	HSMMtube	muscle
33	chr4:15496000-15512800	Weak transcription	Colon Smooth Muscle	Colon
34	chr4:15496200-15501000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:15496200-15502400	Weak transcription	Fetal Stomach	stomach
36	chr4:15498000-15498800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr4:15498200-15499200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
38	chr4:15498200-15538400	Weak transcription	Fetal Heart	heart
39	chr4:15498400-15499000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:15498400-15499000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
41	chr4:15498400-15499000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
42	chr4:15498400-15499000	ZNF genes & repeats	Fetal Lung	lung
43	chr4:15498400-15499000	ZNF genes & repeats	Fetal Muscle Leg	muscle
44	chr4:15498600-15498800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
45	chr4:15498600-15499000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
46	chr4:15498600-15499200	ZNF genes & repeats	Liver	Liver

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