Variant report

Variant	rs12498478
Chromosome Location	chr4:15989660-15989661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15989164..15991988-chr7:91873998..91876151,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000001631	Chromatin interaction
ENSG00000001629	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12512355	0.82[EUR][1000 genomes]
rs12649852	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13142480	0.81[EUR][1000 genomes]
rs17477869	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240682	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3796855	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3815344	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55951685	0.92[ASN][1000 genomes]
rs62290169	0.83[ASN][1000 genomes]
rs6825026	0.83[ASN][1000 genomes]
rs71649933	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv916742	chr4:15797994-16064232	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv461281	chr4:15984033-16001378	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv593770	chr4:15984033-16001378	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15964600-16031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:15968000-16002600	Weak transcription	Left Ventricle	heart
3	chr4:15968600-15993600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:15968800-15992600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:15969600-15990000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:15969600-16011600	Weak transcription	Fetal Lung	lung
7	chr4:15971000-15992200	Weak transcription	Fetal Brain Male	brain
8	chr4:15971000-16008000	Weak transcription	Aorta	Aorta
9	chr4:15973200-15993800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:15974000-15991800	Weak transcription	Fetal Intestine Small	intestine
11	chr4:15976800-16002600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:15977000-16007400	Weak transcription	Gastric	stomach
13	chr4:15978000-15996800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:15978200-16003200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:15978800-16002800	Weak transcription	Right Ventricle	heart
16	chr4:15979400-16000400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr4:15979600-15996600	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr4:15979600-15998800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:15982200-16008200	Weak transcription	Brain Germinal Matrix	brain
20	chr4:15982600-15994400	Weak transcription	Fetal Intestine Large	intestine
21	chr4:15982800-16000200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:15983200-15992800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr4:15983200-15993000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:15983200-16000000	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:15983400-15999800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:15983600-15992800	Strong transcription	Primary hematopoietic stem cells	blood
27	chr4:15983600-15992800	Strong transcription	Fetal Muscle Leg	muscle
28	chr4:15985200-15990600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:15985400-15997000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:15986000-15990000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:15986200-15990000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr4:15987000-16003000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:15987400-15992400	Weak transcription	Fetal Brain Female	brain
34	chr4:15988400-16033800	Weak transcription	Pancreas	Pancrea
35	chr4:15988800-15989800	Weak transcription	Stomach Mucosa	stomach
36	chr4:15988800-15990000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr4:15988800-15991000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:15988800-15992800	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr4:15988800-15995200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr4:15988800-15997000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:15989000-15990800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:15989000-15992000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:15989000-15992200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:15989000-16008000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr4:15989000-16014400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:15989000-16024200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:15989200-15991200	Weak transcription	Colonic Mucosa	Colon
48	chr4:15989400-15989800	Weak transcription	Fetal Stomach	stomach
49	chr4:15989400-15990600	Weak transcription	Rectal Mucosa Donor 29	rectum

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