Variant report

Variant	rs28464608
Chromosome Location	chr4:110475892-110475893
allele	A/G
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	STAT3	chr4:110475809-110475978	MCF10A-Er-Src	breast:	n/a	n/a
2	CEBPB	chr4:110475705-110476008	HepG2	liver:	n/a	chr4:110475837-110475848

Variant related genes	Relation type
CDC42P4	TF binding region
SETP20	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10005225	0.82[AFR][1000 genomes]
rs2062969	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2062970	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28621449	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56761640	0.93[AMR][1000 genomes]
rs59352649	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6533435	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6533436	0.84[AMR][1000 genomes]
rs6812670	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6830772	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6833892	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6837083	0.86[AFR][1000 genomes]
rs72898791	0.88[AFR][1000 genomes]
rs7680129	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7685647	0.88[AFR][1000 genomes]
rs7692819	1.00[EUR][1000 genomes]
rs9884194	0.97[AFR][1000 genomes];1.00[AMR][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	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv980240	chr4:110467259-110476042	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110423400-110480800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:110448800-110479600	Weak transcription	Small Intestine	intestine
3	chr4:110448800-110480000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:110452400-110480800	Weak transcription	Right Ventricle	heart
5	chr4:110454000-110480600	Weak transcription	NHLF	lung
6	chr4:110454600-110480200	Weak transcription	A549	lung
7	chr4:110455600-110480600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:110456400-110480600	Weak transcription	Brain Substantia Nigra	brain
9	chr4:110456400-110481600	Weak transcription	Fetal Heart	heart
10	chr4:110457400-110480600	Weak transcription	Right Atrium	heart
11	chr4:110460200-110480800	Weak transcription	Brain Anterior Caudate	brain
12	chr4:110461000-110480600	Weak transcription	HSMMtube	muscle
13	chr4:110461200-110479600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr4:110462000-110478400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:110462600-110479600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr4:110462800-110480800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:110463200-110480800	Weak transcription	Colonic Mucosa	Colon
18	chr4:110464000-110476200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:110464400-110478800	Weak transcription	Dnd41	blood
20	chr4:110464600-110476000	Weak transcription	Thymus	Thymus
21	chr4:110464600-110480600	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:110464600-110480600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:110464800-110480200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr4:110464800-110480800	Weak transcription	Gastric	stomach
25	chr4:110465400-110480600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr4:110465400-110480600	Weak transcription	Fetal Muscle Leg	muscle
27	chr4:110465600-110480600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr4:110465800-110480200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:110467800-110478800	Weak transcription	Fetal Stomach	stomach
30	chr4:110467800-110480400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr4:110467800-110480800	Weak transcription	Left Ventricle	heart
32	chr4:110468200-110480200	Weak transcription	GM12878-XiMat	blood
33	chr4:110468400-110480800	Weak transcription	Liver	Liver
34	chr4:110469600-110480600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr4:110469800-110480600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:110469800-110480600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr4:110470000-110476000	Weak transcription	HSMM	muscle
38	chr4:110470000-110480200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr4:110470200-110476200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:110470200-110478400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:110470200-110480000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:110470200-110480000	Weak transcription	Primary T cells from cord blood	blood
43	chr4:110470400-110480200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:110470400-110480400	Weak transcription	Primary B cells from cord blood	blood
45	chr4:110470400-110480400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr4:110470400-110480800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:110470600-110479400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr4:110470600-110480400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:110470800-110478600	Weak transcription	HMEC	breast
50	chr4:110470800-110480200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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