Variant report

Variant	rs28535968
Chromosome Location	chr4:3391258-3391259
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3385272..3387718-chr4:3389014..3391654,3	MCF-7	breast:
2	chr4:3388642..3391528-chr4:3405332..3407484,2	MCF-7	breast:
3	chr4:3356602..3361196-chr4:3388835..3391854,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10007038	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10035011	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10049879	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13435851	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1406673	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16844254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16844260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16844272	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28410709	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28420539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28457232	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28489501	0.85[AFR][1000 genomes]
rs28505211	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28636983	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58249502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61527677	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446736	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446737	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446738	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446739	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6812029	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6825183	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6829410	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6847900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73792009	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73792011	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73792031	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73792038	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7656119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv428435	chr4:3386773-3623321	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3386200-3391400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:3386600-3392400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:3386600-3393800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:3386800-3393600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr4:3386800-3393600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:3386800-3395800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:3387600-3392600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:3388000-3394400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:3388400-3392000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr4:3388400-3393600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:3388600-3392000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr4:3388600-3392400	Enhancers	Fetal Muscle Trunk	muscle
13	chr4:3388600-3394400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:3388800-3391400	Enhancers	Fetal Heart	heart
15	chr4:3388800-3391600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr4:3388800-3391800	Enhancers	Fetal Muscle Leg	muscle
17	chr4:3388800-3392000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr4:3388800-3392600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr4:3388800-3392600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:3388800-3392800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:3388800-3394400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr4:3389000-3391600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr4:3389000-3391800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:3389000-3393400	Enhancers	Brain Germinal Matrix	brain
25	chr4:3389200-3391400	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr4:3389200-3391400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:3389200-3391400	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr4:3389200-3395000	Weak transcription	HepG2	liver
29	chr4:3389200-3403400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr4:3389400-3391600	Flanking Active TSS	Osteobl	bone
31	chr4:3389600-3391400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr4:3389600-3391400	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr4:3389600-3391600	Active TSS	Rectal Smooth Muscle	rectum
34	chr4:3389800-3391400	Active TSS	Brain Hippocampus Middle	brain
35	chr4:3390000-3391400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:3390000-3391400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:3390000-3391600	Enhancers	Brain Cingulate Gyrus	brain
38	chr4:3390000-3391600	Weak transcription	Pancreas	Pancrea
39	chr4:3390000-3393400	Enhancers	Placenta	Placenta
40	chr4:3390000-3404600	Weak transcription	Left Ventricle	heart
41	chr4:3390000-3417200	Weak transcription	Gastric	stomach
42	chr4:3390200-3391400	Flanking Active TSS	HMEC	breast
43	chr4:3390200-3391600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:3390200-3394200	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr4:3390200-3398600	Weak transcription	Brain Angular Gyrus	brain
46	chr4:3390400-3391400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:3390400-3391400	Flanking Active TSS	HSMM	muscle
48	chr4:3390400-3391400	Flanking Active TSS	HSMMtube	muscle
49	chr4:3390400-3391400	Flanking Active TSS	NHEK	skin
50	chr4:3390600-3391400	Flanking Active TSS	Primary hematopoietic stem cells	blood

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