Variant report

Variant	rs17083038
Chromosome Location	chr4:54425218-54425219
allele	C/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	NFIC	chr4:54424526-54425796	SK-N-SH	brain:	n/a	n/a
2	GATA2	chr4:54424287-54425344	HUVEC	blood vessel:	n/a	chr4:54424889-54424898 chr4:54425266-54425274
3	TCF12	chr4:54424494-54425852	SK-N-SH	brain:	n/a	n/a
4	EP300	chr4:54425129-54425446	SK-N-SH_RA	brain:	n/a	n/a
5	EP300	chr4:54424540-54425927	SK-N-SH	brain:	n/a	chr4:54424887-54424896
6	PBX3	chr4:54424361-54425474	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr4:54424542-54425920	SK-N-SH	brain:	n/a	chr4:54424889-54424898 chr4:54425266-54425274
8	JUND	chr4:54424076-54425890	SK-N-SH	brain:	n/a	chr4:54424887-54424897 chr4:54424887-54424897 chr4:54424888-54424897 chr4:54424887-54424897 chr4:54424886-54424897 chr4:54424887-54424897
9	FOSL2	chr4:54424584-54425221	SK-N-SH	brain:	n/a	chr4:54424887-54424897 chr4:54424887-54424897 chr4:54424888-54424897 chr4:54424887-54424897 chr4:54424887-54424897
10	FOS	chr4:54424404-54425744	HUVEC	blood vessel:	n/a	chr4:54424887-54424897 chr4:54424887-54424897 chr4:54424886-54424897 chr4:54424888-54424897 chr4:54424887-54424897 chr4:54424887-54424897
11	PBX3	chr4:54424400-54425784	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr4:54424544-54425845	SK-N-SH	brain:	n/a	chr4:54424889-54424898 chr4:54425266-54425274
13	TEAD4	chr4:54424592-54425772	SK-N-SH	brain:	n/a	n/a
14	TCF12	chr4:54424559-54425827	SK-N-SH	brain:	n/a	n/a
15	FOS	chr4:54424678-54425773	MCF10A-Er-Src	breast:	n/a	chr4:54424887-54424897 chr4:54424887-54424897 chr4:54424886-54424897 chr4:54424888-54424897 chr4:54424887-54424897 chr4:54424887-54424897
16	REST	chr4:54423856-54425428	H1-neurons	neurons:	n/a	chr4:54424625-54424638 chr4:54424621-54424641

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54422826..54425638-chr4:54441599..54444250,2	MCF-7	breast:

Variant related genes	Relation type
LNX1	TF binding region
ENSG00000173966	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10007397	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10031491	0.96[AFR][1000 genomes]
rs57991612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9654328	0.95[AFR][1000 genomes];1.00[AMR][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	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54390400-54430400	Weak transcription	Stomach Mucosa	stomach
2	chr4:54409200-54427000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:54412200-54442400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:54413800-54426000	Weak transcription	Right Ventricle	heart
5	chr4:54416000-54438000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:54419800-54430400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:54420000-54437600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:54421400-54428400	Weak transcription	Fetal Stomach	stomach
9	chr4:54421400-54437600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:54421600-54437000	Weak transcription	Pancreas	Pancrea
11	chr4:54423800-54425400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:54423800-54425400	Enhancers	Fetal Muscle Leg	muscle
13	chr4:54423800-54426000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:54423800-54426000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:54423800-54426000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:54424000-54425400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:54424000-54425400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr4:54424000-54425400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:54424000-54425400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr4:54424000-54425400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:54424000-54425400	Strong transcription	Liver	Liver
22	chr4:54424000-54425400	Flanking Active TSS	HUVEC	blood vessel
23	chr4:54424000-54425800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:54424000-54425800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:54424000-54425800	Enhancers	NH-A	brain
26	chr4:54424000-54426400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:54424200-54425400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr4:54424200-54425400	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr4:54424400-54425400	Enhancers	Fetal Brain Male	brain
30	chr4:54424400-54425800	Enhancers	Osteobl	bone
31	chr4:54424600-54425400	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr4:54424600-54425400	Enhancers	H9 Cell Line	embryonic stem cell
33	chr4:54424600-54425400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr4:54424600-54425400	Enhancers	Hela-S3	cervix
35	chr4:54424600-54425400	Flanking Active TSS	NHEK	skin
36	chr4:54424600-54425800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:54424600-54425800	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr4:54424600-54426000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:54424600-54430200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:54424600-54430400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr4:54424600-54430600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:54424800-54425400	Enhancers	NHLF	lung
43	chr4:54424800-54425800	Enhancers	HSMM	muscle
44	chr4:54424800-54426200	Enhancers	HMEC	breast
45	chr4:54425000-54425600	Enhancers	NHDF-Ad	bronchial
46	chr4:54425000-54425800	Enhancers	Muscle Satellite Cultured Cells	--
47	chr4:54425200-54425400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr4:54425200-54425400	Enhancers	Brain Anterior Caudate	brain
49	chr4:54425200-54425400	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr4:54425200-54425400	Strong transcription	Rectal Mucosa Donor 31	rectum

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