Variant report

Variant	rs56721656
Chromosome Location	chr1:228640243-228640244
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	CBX3	chr1:228639874-228640817	K562	blood:	n/a	n/a
2	EP300	chr1:228640023-228640724	A549	lung:	n/a	n/a
3	USF2	chr1:228640236-228640584	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:228639909-228642215	K562	blood:	n/a	n/a
5	RXRA	chr1:228640163-228640617	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:228639678-228642181	Hela-S3	cervix:	n/a	n/a
7	JUN	chr1:228639464-228641509	K562	blood:	n/a	chr1:228640231-228640241 chr1:228640230-228640242 chr1:228640231-228640241 chr1:228640054-228640062 chr1:228640231-228640241 chr1:228640232-228640240
8	MAFF	chr1:228640227-228640489	HepG2	liver:	n/a	n/a
9	GATA3	chr1:228639973-228640740	A549	lung:	n/a	n/a
10	EP300	chr1:228640148-228640444	HepG2	liver:	n/a	n/a
11	JUND	chr1:228639863-228640673	K562	blood:	n/a	chr1:228640359-228640370 chr1:228640231-228640241 chr1:228640230-228640242 chr1:228640231-228640241 chr1:228640054-228640062 chr1:228640231-228640241 chr1:228640232-228640240
12	RXRA	chr1:228640114-228640540	HepG2	liver:	n/a	n/a
13	GABPA	chr1:228640116-228640657	K562	blood:	n/a	n/a
14	POLR2A	chr1:228639882-228641003	K562	blood:	n/a	n/a
15	JUND	chr1:228640133-228640590	Hela-S3	cervix:	n/a	chr1:228640359-228640370 chr1:228640231-228640241 chr1:228640230-228640242 chr1:228640231-228640241 chr1:228640231-228640241 chr1:228640232-228640240
16	RXRA	chr1:228639720-228640773	SK-N-SH	brain:	n/a	n/a
17	MAZ	chr1:228639941-228640671	K562	blood:	n/a	chr1:228640075-228640085
18	FOSL1	chr1:228640060-228640615	K562	blood:	n/a	chr1:228640231-228640241 chr1:228640230-228640242 chr1:228640231-228640241 chr1:228640359-228640370 chr1:228640231-228640241 chr1:228640232-228640240
19	POLR2A	chr1:228640038-228640416	MCF-7	breast:	n/a	n/a
20	FOS	chr1:228640125-228640651	K562	blood:	n/a	chr1:228640231-228640241 chr1:228640230-228640242 chr1:228640231-228640241 chr1:228640231-228640241 chr1:228640232-228640240
21	ZMIZ1	chr1:228639895-228640692	K562	blood:	n/a	n/a
22	MAFK	chr1:228640210-228640459	HepG2	liver:	n/a	chr1:228640230-228640240 chr1:228640230-228640239
23	JUN	chr1:228640138-228640628	K562	blood:	n/a	chr1:228640231-228640241 chr1:228640230-228640242 chr1:228640231-228640241 chr1:228640231-228640241 chr1:228640232-228640240
24	ZBTB7A	chr1:228640074-228640299	HepG2	liver:	n/a	n/a
25	MAZ	chr1:228640127-228640429	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:228640087-228642351	K562	blood:	n/a	n/a
27	MAX	chr1:228639901-228640561	K562	blood:	n/a	chr1:228640075-228640085
28	POLR2A	chr1:228639922-228642237	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAFF	chr1:228640167-228640514	K562	blood:	n/a	n/a
30	BHLHE40	chr1:228640065-228640572	K562	blood:	n/a	n/a
31	RCOR1	chr1:228640032-228640642	K562	blood:	n/a	n/a
32	MAX	chr1:228640198-228640554	K562	blood:	n/a	n/a
33	NR2F2	chr1:228639950-228640684	HepG2	liver:	n/a	n/a
34	POLR2A	chr1:228640166-228640250	H1-hESC	embryonic stem cell:	n/a	n/a
35	RXRA	chr1:228639995-228640776	SK-N-SH	brain:	n/a	n/a
36	FOSL2	chr1:228640076-228640675	A549	lung:	n/a	chr1:228640231-228640241 chr1:228640230-228640242 chr1:228640231-228640241 chr1:228640231-228640241 chr1:228640232-228640240
37	JUN	chr1:228640129-228640601	K562	blood:	n/a	chr1:228640231-228640241 chr1:228640230-228640242 chr1:228640231-228640241 chr1:228640231-228640241 chr1:228640232-228640240
38	POLR2A	chr1:228639912-228642257	H1-hESC	embryonic stem cell:	n/a	n/a
39	ATF3	chr1:228640152-228640629	K562	blood:	n/a	n/a
40	RCOR1	chr1:228640031-228640564	K562	blood:	n/a	n/a
41	CEBPD	chr1:228639953-228642416	K562	blood:	n/a	n/a
42	EGR1	chr1:228640161-228640600	K562	blood:	n/a	n/a
43	BCLAF1	chr1:228640187-228642462	K562	blood:	n/a	chr1:228641384-228641393
44	HDAC2	chr1:228640196-228640746	K562	blood:	n/a	n/a
45	HMGN3	chr1:228640040-228640853	K562	blood:	n/a	n/a
46	ARID3A	chr1:228640226-228640376	HepG2	liver:	n/a	n/a
47	NR2F2	chr1:228639931-228640785	HepG2	liver:	n/a	n/a
48	BACH1	chr1:228640207-228640427	K562	blood:	n/a	n/a
49	USF1	chr1:228640173-228640636	K562	blood:	n/a	n/a
50	RCOR1	chr1:228640226-228640472	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228638761..228647671-chr1:228695176..228704605,18	K562	blood:
2	chr1:228589639..228603795-chr1:228638211..228648676,43	MCF-7	breast:
3	chr1:228527085..228530281-chr1:228640175..228642076,3	K562	blood:
4	chr1:228616675..228619300-chr1:228638219..228642365,5	MCF-7	breast:
5	chr1:228640213..228643182-chr1:228687753..228691528,4	K562	blood:
6	chr1:228462628..228466791-chr1:228639657..228643732,4	K562	blood:
7	chr1:228565749..228568495-chr1:228638648..228642089,3	K562	blood:
8	chr1:228275073..228277944-chr1:228639266..228642188,2	K562	blood:

Variant related genes	Relation type
ENSG00000230841	TF binding region
ENSG00000215811	Chromatin interaction
ENSG00000154358	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000162931	Chromatin interaction
ENSG00000231563	Chromatin interaction
ENSG00000269934	Chromatin interaction
ENSG00000154370	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10916315	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916316	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916318	1.00[EUR][1000 genomes]
rs10916319	1.00[EUR][1000 genomes]
rs12091870	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16841344	0.89[EUR][1000 genomes]
rs16848618	0.89[EUR][1000 genomes]
rs2104436	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291998	0.89[EUR][1000 genomes]
rs34297060	0.89[EUR][1000 genomes]
rs3738688	0.89[EUR][1000 genomes]
rs4653550	0.89[EUR][1000 genomes]
rs4653952	0.89[EUR][1000 genomes]
rs4653953	0.89[EUR][1000 genomes]
rs4653957	0.89[EUR][1000 genomes]
rs4653958	0.89[EUR][1000 genomes]
rs4653961	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653963	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56895565	0.89[EUR][1000 genomes]
rs58110358	0.89[EUR][1000 genomes]
rs59225017	0.89[EUR][1000 genomes]
rs60640636	0.89[EUR][1000 genomes]
rs6679518	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6690116	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511681	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528331	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
9	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
10	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv873281	chr1:228505739-228656780	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
12	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
13	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
14	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228634000-228643200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:228634200-228641600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:228634200-228643000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:228634200-228644800	Weak transcription	Gastric	stomach
5	chr1:228634400-228641600	Weak transcription	Brain Angular Gyrus	brain
6	chr1:228634400-228644200	Weak transcription	Brain Anterior Caudate	brain
7	chr1:228634400-228644600	Weak transcription	Right Atrium	heart
8	chr1:228634400-228644600	Weak transcription	Right Ventricle	heart
9	chr1:228635000-228640600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:228635000-228641400	Weak transcription	Brain Germinal Matrix	brain
11	chr1:228635000-228641600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:228635000-228642000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:228635200-228643000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:228635200-228644200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:228635600-228641400	Weak transcription	Fetal Brain Female	brain
16	chr1:228635800-228643000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:228636600-228641200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:228637000-228641600	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:228637400-228643000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:228637600-228643400	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:228638000-228643000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:228638200-228643200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:228638400-228643400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:228638400-228644600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:228638800-228644600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:228639000-228643200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:228639200-228641400	Strong transcription	Fetal Intestine Small	intestine
28	chr1:228639600-228640400	Enhancers	HepG2	liver
29	chr1:228639600-228641200	Weak transcription	Fetal Intestine Large	intestine
30	chr1:228639600-228642000	Enhancers	K562	blood
31	chr1:228639600-228642200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:228639800-228640400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr1:228639800-228640600	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr1:228639800-228640800	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr1:228639800-228641000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:228639800-228641000	Enhancers	Hela-S3	cervix
37	chr1:228639800-228641800	Enhancers	Spleen	Spleen
38	chr1:228639800-228642200	Enhancers	A549	lung
39	chr1:228640000-228640400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:228640000-228640400	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr1:228640000-228640600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:228640000-228640600	Enhancers	NHDF-Ad	bronchial
43	chr1:228640000-228641000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr1:228640000-228641600	Genic enhancers	Placenta	Placenta
45	chr1:228640000-228643000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:228640000-228643400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:228640000-228644000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:228640200-228640400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:228640200-228640400	Enhancers	Fetal Brain Male	brain
50	chr1:228640200-228640400	Enhancers	NHLF	lung

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