Variant report

Variant	rs10023609
Chromosome Location	chr4:652883-652884
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	ARID3A	chr4:652831-653271	HepG2	liver:	n/a	n/a
2	RCOR1	chr4:652802-653424	HepG2	liver:	n/a	n/a
3	JUND	chr4:652814-653201	HepG2	liver:	n/a	n/a
4	FOXA1	chr4:652671-653343	HepG2	liver:	n/a	n/a
5	MAX	chr4:652724-653576	HepG2	liver:	n/a	chr4:653422-653432 chr4:653369-653379 chr4:652843-652852 chr4:653434-653444 chr4:653412-653422
6	TCF12	chr4:652868-653420	HepG2	liver:	n/a	n/a
7	CHD2	chr4:652751-652986	HepG2	liver:	n/a	n/a
8	NFIC	chr4:652755-653269	HepG2	liver:	n/a	n/a
9	EP300	chr4:652790-653234	HepG2	liver:	n/a	n/a
10	EP300	chr4:652811-653280	HepG2	liver:	n/a	n/a
11	MYBL2	chr4:652653-653326	HepG2	liver:	n/a	n/a
12	BHLHE40	chr4:652747-653269	HepG2	liver:	n/a	n/a
13	RXRA	chr4:652778-653192	HepG2	liver:	n/a	n/a
14	FOXA2	chr4:652511-653380	HepG2	liver:	n/a	n/a
15	FOXA2	chr4:652853-653231	HepG2	liver:	n/a	n/a
16	MAX	chr4:652437-653567	HepG2	liver:	n/a	chr4:653422-653432 chr4:653369-653379 chr4:652843-652852 chr4:653434-653444 chr4:653412-653422
17	REST	chr4:652772-653251	HepG2	liver:	n/a	n/a
18	MXI1	chr4:652723-653579	HepG2	liver:	n/a	n/a
19	FOXA1	chr4:652659-653376	HepG2	liver:	n/a	n/a
20	SP1	chr4:652774-653334	HepG2	liver:	n/a	n/a
21	FOXA1	chr4:652691-653262	HepG2	liver:	n/a	n/a
22	FOXA1	chr4:652740-653259	HepG2	liver:	n/a	n/a
23	MYC	chr4:652883-652921	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:641525..644066-chr4:652058..654958,2	K562	blood:
2	chr4:647827..650169-chr4:651801..653823,2	K562	blood:
3	chr4:613849..616261-chr4:650426..653017,2	K562	blood:

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

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10001451	1.00[AMR][1000 genomes]
rs10006278	1.00[AMR][1000 genomes]
rs10010598	1.00[AMR][1000 genomes]
rs10017347	1.00[AMR][1000 genomes]
rs10017435	1.00[AMR][1000 genomes]
rs10018607	1.00[AMR][1000 genomes]
rs10020292	1.00[AMR][1000 genomes]
rs10024023	1.00[AMR][1000 genomes]
rs10025758	1.00[AMR][1000 genomes]
rs10027392	1.00[AMR][1000 genomes]
rs10028157	1.00[AMR][1000 genomes]
rs10028526	1.00[AMR][1000 genomes]
rs10028537	1.00[AMR][1000 genomes]
rs10029924	1.00[AMR][1000 genomes]
rs10030020	1.00[AMR][1000 genomes]
rs10035021	1.00[AMR][1000 genomes]
rs12331186	1.00[AMR][1000 genomes]
rs28366852	1.00[AMR][1000 genomes]
rs28399001	1.00[AMR][1000 genomes]
rs28413992	1.00[AMR][1000 genomes]
rs28414606	1.00[AMR][1000 genomes]
rs28436699	1.00[AMR][1000 genomes]
rs28459140	1.00[AMR][1000 genomes]
rs28477853	1.00[AMR][1000 genomes]
rs28478159	1.00[AMR][1000 genomes]
rs28510278	1.00[AMR][1000 genomes]
rs28510755	1.00[AMR][1000 genomes]
rs28527330	1.00[AMR][1000 genomes]
rs28531889	1.00[AMR][1000 genomes]
rs28538930	1.00[AMR][1000 genomes]
rs28540058	1.00[AMR][1000 genomes]
rs28546458	1.00[AMR][1000 genomes]
rs28551514	1.00[AMR][1000 genomes]
rs28601829	1.00[AMR][1000 genomes]
rs28605120	1.00[AMR][1000 genomes]
rs28615478	1.00[AMR][1000 genomes]
rs28633819	1.00[AMR][1000 genomes]
rs28665728	1.00[AMR][1000 genomes]
rs28671384	1.00[AMR][1000 genomes]
rs28706206	1.00[AMR][1000 genomes]
rs28709824	1.00[AMR][1000 genomes]
rs28754367	1.00[AMR][1000 genomes]
rs28818828	1.00[AMR][1000 genomes]
rs28843467	1.00[AMR][1000 genomes]
rs28862677	1.00[AMR][1000 genomes]
rs6827034	1.00[AMR][1000 genomes]
rs6835327	1.00[AMR][1000 genomes]
rs6842140	1.00[AMR][1000 genomes]
rs73056559	1.00[AMR][1000 genomes]
rs7655485	1.00[AMR][1000 genomes]
rs7665160	1.00[AMR][1000 genomes]
rs7671294	1.00[AMR][1000 genomes]
rs7680416	1.00[AMR][1000 genomes]
rs7689014	1.00[AMR][1000 genomes]
rs7696942	1.00[AMR][1000 genomes]
rs9990446	1.00[AMR][1000 genomes]
rs9991058	1.00[AMR][1000 genomes]
rs9994679	1.00[AMR][1000 genomes]
rs9995112	1.00[AMR][1000 genomes]
rs9996316	1.00[AMR][1000 genomes]
rs9996400	1.00[AMR][1000 genomes]
rs9998466	1.00[AMR][1000 genomes]
rs9998594	1.00[AMR][1000 genomes]
rs9998776	1.00[AMR][1000 genomes]
rs9999833	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	esv3428482	chr4:651252-655450	Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	esv3361501	chr4:651652-655150	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	esv3363115	chr4:651852-655150	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	esv3409588	chr4:652502-655300	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:631400-657000	Weak transcription	Right Atrium	heart
2	chr4:641800-657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:642400-654600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:642800-657000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:643000-657000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:645800-656800	Weak transcription	Gastric	stomach
7	chr4:648400-657000	Weak transcription	Right Ventricle	heart
8	chr4:648800-653400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:649200-653000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:649800-653200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:649800-655600	Weak transcription	Thymus	Thymus
12	chr4:650000-653200	Weak transcription	Fetal Brain Female	brain
13	chr4:650000-654000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:650000-654200	Enhancers	HepG2	liver
15	chr4:650800-656000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr4:651000-653200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:651000-653600	Weak transcription	Fetal Brain Male	brain
18	chr4:651200-653200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr4:651200-654400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:651400-653000	Enhancers	Lung	lung
21	chr4:651400-653200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:651400-653200	Weak transcription	Dnd41	blood
23	chr4:651400-653400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:651400-656400	Weak transcription	Pancreas	Pancrea
25	chr4:651600-653200	Weak transcription	Fetal Intestine Small	intestine
26	chr4:651600-657000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr4:651600-657200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr4:651800-653200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr4:651800-656800	Weak transcription	Primary B cells from cord blood	blood
30	chr4:652000-653600	Weak transcription	Fetal Stomach	stomach
31	chr4:652000-656800	Weak transcription	Fetal Lung	lung
32	chr4:652200-654000	Genic enhancers	Spleen	Spleen
33	chr4:652400-655200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:652400-656800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr4:652600-654000	Strong transcription	Brain Anterior Caudate	brain
36	chr4:652600-656800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr4:652600-656800	Weak transcription	Fetal Thymus	thymus
38	chr4:652800-653600	Strong transcription	Primary T cells from cord blood	blood
39	chr4:652800-653600	Strong transcription	Brain Angular Gyrus	brain
40	chr4:652800-653600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
41	chr4:652800-653800	Strong transcription	Brain Hippocampus Middle	brain
42	chr4:652800-654000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr4:652800-654400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:652800-654400	Strong transcription	Brain Substantia Nigra	brain
45	chr4:652800-656000	Strong transcription	Brain Germinal Matrix	brain

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