Variant report

Variant	rs28438722
Chromosome Location	chr4:657060-657061
allele	C/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	MXI1	chr4:656777-658347	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr4:657056-657858	SK-N-MC	brain:	n/a	n/a
3	ELF1	chr4:657030-658394	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:646849..649113-chr4:654761..657491,3	K562	blood:
2	chr4:644054..646414-chr4:656838..659721,2	MCF-7	breast:

Variant related genes	Relation type
PDE6B	TF binding region
ENSG00000272927	TF binding region
ENSG00000133256	Chromatin interaction
ENSG00000242686	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10014936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10023220	1.00[AMR][1000 genomes]
rs10050278	0.91[AFR][1000 genomes]
rs28483058	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription 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	41 gene(s)	inside rSNPs	diseases
7	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
9	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS 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	40 gene(s)	inside rSNPs	diseases
12	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS 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	104 gene(s)	inside rSNPs	diseases
14	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv4194	chr4:635316-657212	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv878248	chr4:645300-685993	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	nsv878249	chr4:649639-691026	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	esv1829397	chr4:655939-1041957	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:651600-657200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:655600-657200	Enhancers	Spleen	Spleen
3	chr4:656000-657200	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr4:656400-657200	Enhancers	Esophagus	oesophagus
5	chr4:656600-657400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:656600-657400	Flanking Active TSS	Brain Germinal Matrix	brain
7	chr4:656800-657200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:656800-657200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
9	chr4:656800-657200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:656800-657200	Flanking Active TSS	Colonic Mucosa	Colon
11	chr4:656800-657200	Enhancers	Fetal Heart	heart
12	chr4:656800-657200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
13	chr4:656800-657400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr4:656800-657400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr4:656800-657400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr4:656800-657400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr4:656800-657400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:656800-657400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr4:656800-657400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:656800-657400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr4:656800-657400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:656800-657400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:656800-657400	Active TSS	Brain Anterior Caudate	brain
24	chr4:656800-657400	Flanking Active TSS	Brain Cingulate Gyrus	brain
25	chr4:656800-657400	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr4:656800-657400	Flanking Active TSS	Fetal Intestine Small	intestine
27	chr4:656800-657400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
28	chr4:656800-657400	Flanking Active TSS	Fetal Thymus	thymus
29	chr4:656800-657400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
30	chr4:656800-657600	Flanking Active TSS	Fetal Brain Female	brain
31	chr4:656800-657600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
32	chr4:656800-658200	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr4:656800-658200	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr4:656800-658200	Flanking Active TSS	Pancreas	Pancrea
35	chr4:656800-658400	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr4:656800-658400	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr4:656800-658400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr4:656800-658400	Active TSS	Fetal Intestine Large	intestine
39	chr4:656800-658800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:657000-657200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
41	chr4:657000-657200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:657000-657200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:657000-657200	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:657000-657200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr4:657000-657200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:657000-657200	Flanking Active TSS	Brain Substantia Nigra	brain
47	chr4:657000-657200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
48	chr4:657000-657200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
49	chr4:657000-657200	Enhancers	Placenta	Placenta
50	chr4:657000-657200	Flanking Active TSS	Ovary	ovary

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