Variant report

Variant	rs72616962
Chromosome Location	chr4:128801044-128801045
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:128801042-128803191	GM12891	blood:	n/a	n/a
2	ZNF384	chr4:128800943-128801221	K562	blood:	n/a	n/a
3	GTF3C2	chr4:128801027-128802844	K562	blood:	n/a	n/a
4	POLR2A	chr4:128801023-128801356	K562	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:128800019..128803742-chr4:128979765..128984325,9	K562	blood:
2	chr4:128762399..128765265-chr4:128800417..128803235,2	K562	blood:
3	chr4:128799364..128804463-chr4:128885048..128888163,8	K562	blood:
4	chr4:128789472..128793684-chr4:128799349..128802011,4	K562	blood:
5	chr4:128701911..128705042-chr4:128800160..128804699,6	K562	blood:
6	chr4:128799393..128805047-chr4:128807036..128813369,7	MCF-7	breast:
7	chr4:128702203..128705505-chr4:128800773..128804170,4	MCF-7	breast:
8	chr4:128701663..128704492-chr4:128800560..128804784,7	MCF-7	breast:
9	chr4:128686775..128688582-chr4:128798600..128801332,2	K562	blood:
10	chr4:128798970..128804322-chr4:128884774..128888553,10	K562	blood:
11	chr4:128801016..128804523-chr4:128885640..128887927,4	MCF-7	breast:
12	chr4:128800672..128803742-chr4:128979765..128985676,12	K562	blood:
13	chr4:128800896..128803117-chr4:128885374..128888251,3	MCF-7	breast:

No data

Variant related genes	Relation type
PLK4	TF binding region
ENSG00000142731	Chromatin interaction
ENSG00000164070	Chromatin interaction
ENSG00000138709	Chromatin interaction
ENSG00000251821	Chromatin interaction
ENSG00000261668	Chromatin interaction
ENSG00000164074	Chromatin interaction
ENSG00000164073	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10493148	0.92[ASN][1000 genomes]
rs11940642	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1380155	0.86[ASN][1000 genomes]
rs16997978	0.97[ASN][1000 genomes]
rs17012683	0.92[ASN][1000 genomes]
rs17012687	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17012695	0.92[ASN][1000 genomes]
rs17012703	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17012708	0.92[ASN][1000 genomes]
rs17012710	0.92[ASN][1000 genomes]
rs17012727	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17012743	0.95[ASN][1000 genomes]
rs17012747	0.95[ASN][1000 genomes]
rs17012750	0.95[ASN][1000 genomes]
rs17012788	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1841156	0.91[ASN][1000 genomes]
rs1841157	0.91[ASN][1000 genomes]
rs2276898	0.80[ASN][1000 genomes]
rs2276899	0.80[ASN][1000 genomes]
rs2276900	0.80[ASN][1000 genomes]
rs3733319	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4422427	0.94[ASN][1000 genomes]
rs4426798	0.80[ASN][1000 genomes]
rs4431238	0.80[ASN][1000 genomes]
rs4456965	0.92[ASN][1000 genomes]
rs4470641	0.80[ASN][1000 genomes]
rs4508904	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4513584	0.94[ASN][1000 genomes]
rs4607232	0.95[ASN][1000 genomes]
rs4618331	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56250604	0.97[ASN][1000 genomes]
rs56893530	0.94[ASN][1000 genomes]
rs57499646	0.93[ASN][1000 genomes]
rs57561160	0.94[ASN][1000 genomes]
rs57645489	0.92[ASN][1000 genomes]
rs58830700	0.92[ASN][1000 genomes]
rs59189441	0.93[ASN][1000 genomes]
rs59569890	0.84[ASN][1000 genomes]
rs59815828	0.85[ASN][1000 genomes]
rs60279389	0.95[ASN][1000 genomes]
rs60930401	0.88[ASN][1000 genomes]
rs61300521	0.94[ASN][1000 genomes]
rs6850549	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6850726	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72616952	0.86[ASN][1000 genomes]
rs72616953	0.91[ASN][1000 genomes]
rs72616954	0.90[ASN][1000 genomes]
rs72616955	0.86[ASN][1000 genomes]
rs72616956	0.94[ASN][1000 genomes]
rs72616957	0.94[ASN][1000 genomes]
rs72616958	0.94[ASN][1000 genomes]
rs72616959	0.94[ASN][1000 genomes]
rs72616960	0.94[ASN][1000 genomes]
rs72616961	0.94[ASN][1000 genomes]
rs72616963	0.97[ASN][1000 genomes]
rs72616964	0.88[ASN][1000 genomes]
rs72616965	0.94[ASN][1000 genomes]
rs72616966	0.90[ASN][1000 genomes]
rs72616967	0.86[ASN][1000 genomes]
rs72616968	0.88[ASN][1000 genomes]
rs72616969	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72616972	0.80[ASN][1000 genomes]
rs72616973	0.80[ASN][1000 genomes]
rs72616974	0.80[ASN][1000 genomes]
rs72616975	0.80[ASN][1000 genomes]
rs7684815	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv817326	chr4:128292216-128915201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv879917	chr4:128478408-128841252	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv879922	chr4:128554404-128901402	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv879923	chr4:128554404-129068179	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	esv1801492	chr4:128566686-128934513	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv1792644	chr4:128566686-129133826	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	esv1795770	chr4:128566686-129145581	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers 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	44 gene(s)	inside rSNPs	diseases
9	esv1793579	chr4:128577439-128871309	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	esv3431515	chr4:128657260-128932577	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv532740	chr4:128710011-129035335	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	esv3416036	chr4:128782694-129133956	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128791000-128801200	Weak transcription	Primary T cells from cord blood	blood
2	chr4:128792200-128801400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:128792400-128801200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:128792400-128801200	Weak transcription	Adipose Nuclei	Adipose
5	chr4:128792400-128801400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:128792400-128802000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:128792600-128801200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:128792600-128801200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:128792600-128801200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr4:128792600-128801200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:128792600-128801200	Weak transcription	Fetal Intestine Small	intestine
12	chr4:128792600-128801200	Weak transcription	Left Ventricle	heart
13	chr4:128792800-128801200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:128792800-128801800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:128794400-128801200	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:128796800-128801200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr4:128797600-128801200	Weak transcription	NHDF-Ad	bronchial
18	chr4:128799400-128801200	Weak transcription	Right Atrium	heart
19	chr4:128799600-128801200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr4:128799800-128801600	Weak transcription	Ovary	ovary
21	chr4:128800000-128801400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:128800200-128801400	Flanking Active TSS	Dnd41	blood
23	chr4:128800400-128801400	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr4:128800400-128801400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr4:128800400-128803200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:128800400-128803200	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr4:128800600-128801200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr4:128800600-128801200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr4:128800600-128801400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr4:128800600-128801400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr4:128800600-128802600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:128800600-128802800	Active TSS	K562	blood
33	chr4:128800600-128803800	Active TSS	GM12878-XiMat	blood
34	chr4:128800800-128801200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:128800800-128801200	Enhancers	Fetal Thymus	thymus
36	chr4:128801000-128801200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:128801000-128801200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr4:128801000-128801200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:128801000-128801200	Enhancers	Primary B cells from cord blood	blood
40	chr4:128801000-128801200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr4:128801000-128801200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr4:128801000-128801200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:128801000-128801200	Enhancers	Brain Anterior Caudate	brain
44	chr4:128801000-128801200	Enhancers	Brain Substantia Nigra	brain
45	chr4:128801000-128801200	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr4:128801000-128801200	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr4:128801000-128801200	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr4:128801000-128801200	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr4:128801000-128801200	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr4:128801000-128801200	Enhancers	Small Intestine	intestine

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