Variant report

Variant	rs56123640
Chromosome Location	chr1:247374243-247374244
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:366)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:366 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr1:247373641-247374419	HepG2	liver:	n/a	n/a
2	BHLHE40	chr1:247373685-247374462	K562	blood:	n/a	chr1:247373721-247373737
3	SIN3AK20	chr1:247373512-247374468	HCT-116	colon:	n/a	n/a
4	MAX	chr1:247373629-247374449	SK-N-SH	brain:	n/a	n/a
5	MXI1	chr1:247373356-247374638	IMR90	lung:	n/a	n/a
6	CREB1	chr1:247373528-247374543	GM12878	blood:	n/a	n/a
7	SIN3AK20	chr1:247373239-247374467	MCF-7	breast:	n/a	n/a
8	POLR2A	chr1:247373586-247374412	HUVEC	blood vessel:	n/a	n/a
9	ELK4	chr1:247373368-247374358	Hela-S3	cervix:	n/a	n/a
10	TAF1	chr1:247373936-247374293	H1-neurons	neurons:	n/a	n/a
11	TAF1	chr1:247373898-247374269	H1-hESC	embryonic stem cell:	n/a	n/a
12	MXI1	chr1:247373582-247374485	Hela-S3	cervix:	n/a	n/a
13	FOS	chr1:247374107-247374412	MCF10A-Er-Src	breast:	n/a	n/a
14	MXI1	chr1:247372272-247375223	SK-N-SH	brain:	n/a	n/a
15	BRCA1	chr1:247374033-247374397	Hela-S3	cervix:	n/a	n/a
16	SIN3AK20	chr1:247373471-247374399	PANC-1	pancreas:	n/a	n/a
17	ELF1	chr1:247373678-247374454	A549	lung:	n/a	n/a
18	SIN3AK20	chr1:247373906-247374277	PANC-1	pancreas:	n/a	n/a
19	NFYA	chr1:247373807-247374385	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr1:247373912-247374291	H1-hESC	embryonic stem cell:	n/a	n/a
21	TAF1	chr1:247373535-247374400	PFSK-1	brain:	n/a	n/a
22	RAD21	chr1:247373487-247374343	IMR90	lung:	n/a	chr1:247373724-247373737 chr1:247373953-247373963
23	POLR2A	chr1:247373653-247374321	GM12892	blood:	n/a	n/a
24	POLR2A	chr1:247373573-247374483	Hela-S3	cervix:	n/a	n/a
25	SIN3AK20	chr1:247373949-247374263	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr1:247373900-247374407	HCT-116	colon:	n/a	n/a
27	POLR2A	chr1:247373630-247374407	GM12891	blood:	n/a	n/a
28	MAX	chr1:247373539-247374511	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:247373614-247374399	A549	lung:	n/a	n/a
30	SIN3A	chr1:247373539-247374361	GM12878	blood:	n/a	chr1:247373744-247373755
31	CTCF	chr1:247374164-247374534	K562	blood:	n/a	n/a
32	TAF1	chr1:247373572-247374489	K562	blood:	n/a	n/a
33	MYC	chr1:247374031-247374500	MCF10A-Er-Src	breast:	n/a	n/a
34	EP300	chr1:247372831-247374564	K562	blood:	n/a	n/a
35	POLR2A	chr1:247373653-247374430	H1-neurons	neurons:	n/a	n/a
36	MAX	chr1:247373536-247374451	A549	lung:	n/a	n/a
37	RCOR1	chr1:247373965-247374340	HepG2	liver:	n/a	n/a
38	GABPA	chr1:247373526-247374392	HL-60	blood:	n/a	chr1:247373975-247373984
39	SIN3A	chr1:247373528-247374510	H1-hESC	embryonic stem cell:	n/a	chr1:247373744-247373755
40	POLR2A	chr1:247373685-247374479	K562	blood:	n/a	n/a
41	USF1	chr1:247373858-247374416	A549	lung:	n/a	n/a
42	SP1	chr1:247373898-247374501	K562	blood:	n/a	chr1:247373974-247373984 chr1:247373973-247373985 chr1:247373974-247373984 chr1:247373973-247373985 chr1:247373974-247373983 chr1:247373974-247373983 chr1:247373975-247373984
43	POLR2A	chr1:247373793-247374319	HepG2	liver:	n/a	n/a
44	ELF1	chr1:247373643-247374476	A549	lung:	n/a	n/a
45	NFIC	chr1:247373665-247374603	ECC-1	luminal epithelium:	n/a	n/a
46	REST	chr1:247373564-247374356	PFSK-1	brain:	n/a	n/a
47	YY1	chr1:247373951-247374399	K562	blood:	n/a	n/a
48	GATA3	chr1:247373520-247374320	A549	lung:	n/a	n/a
49	POLR2A	chr1:247373830-247374355	SK-N-SH	brain:	n/a	n/a
50	STAT5A	chr1:247373824-247374408	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:247366973..247371599-chr1:247371697..247375755,6	MCF-7	breast:
2	chr1:247373865..247374385-chr1:247494539..247495272,2	NB4	blood:
3	chr1:247373719..247374472-chr17:41465801..41466586,2	Hela-S3	cervix:
4	chr1:247373611..247374330-chr11:47429734..47430575,2	Hela-S3	cervix:
5	chr1:247371907..247375145-chr1:247492885..247497524,4	MCF-7	breast:
6	chr1:247373675..247374500-chr19:12902301..12903055,2	Hela-S3	cervix:
7	chr1:247374235..247377046-chr1:247498080..247500631,2	K562	blood:
8	chr1:247274493..247276812-chr1:247371838..247375899,3	K562	blood:
9	chr1:247371861..247375582-chr1:247493463..247496360,5	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF124-2	chr1:247373993-247374295	ENSG00000232347.1

No data

Variant related genes	Relation type
MIR3916	TF binding region
ENSG00000188825	Chromatin interaction
ENSG00000252516	Chromatin interaction
ENSG00000162714	Chromatin interaction
ENSG00000221953	Chromatin interaction
ENSG00000165915	Chromatin interaction
ENSG00000171223	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12083552	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17720872	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41305576	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55932854	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56036028	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56130102	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56212015	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56358623	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61087736	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72770359	0.83[AMR][1000 genomes]
rs72770361	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72770366	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72770367	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72770371	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72770374	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72770379	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72770384	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72770390	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72770391	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
3	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
6	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
8	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
9	nsv873436	chr1:247339064-247385877	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247372600-247374400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:247372600-247374600	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr1:247372800-247374400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:247372800-247374400	Active TSS	HSMM	muscle
5	chr1:247372800-247374600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:247373000-247374400	Active TSS	H1 Cell Line	embryonic stem cell
7	chr1:247373000-247374400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr1:247373000-247374400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:247373000-247374400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:247373000-247374400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:247373000-247374400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:247373000-247374400	Active TSS	Ovary	ovary
13	chr1:247373000-247374400	Active TSS	A549	lung
14	chr1:247373000-247374400	Active TSS	NHDF-Ad	bronchial
15	chr1:247373000-247374600	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr1:247373000-247374600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:247373000-247374600	Active TSS	GM12878-XiMat	blood
18	chr1:247373200-247374400	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr1:247373200-247374400	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:247373200-247374400	Active TSS	Muscle Satellite Cultured Cells	--
21	chr1:247373200-247374400	Active TSS	Fetal Intestine Small	intestine
22	chr1:247373200-247374400	Active TSS	Fetal Kidney	kidney
23	chr1:247373200-247374400	Active TSS	Rectal Smooth Muscle	rectum
24	chr1:247373200-247374400	Active TSS	HSMMtube	muscle
25	chr1:247373200-247374600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:247373200-247374600	Active TSS	Fetal Brain Female	brain
27	chr1:247373200-247374600	Active TSS	Thymus	Thymus
28	chr1:247373200-247374800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:247373200-247374800	Active TSS	HepG2	liver
30	chr1:247373400-247374400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:247373400-247374400	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr1:247373400-247374400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr1:247373400-247374400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:247373400-247374400	Active TSS	Brain Hippocampus Middle	brain
35	chr1:247373400-247374400	Active TSS	Colon Smooth Muscle	Colon
36	chr1:247373400-247374400	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr1:247373400-247374400	Active TSS	Esophagus	oesophagus
38	chr1:247373400-247374400	Active TSS	Placenta Amnion	Placenta Amnion
39	chr1:247373400-247374400	Active TSS	NHLF	lung
40	chr1:247373400-247374600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:247373400-247374600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:247373400-247374600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:247373400-247374600	Active TSS	Fetal Intestine Large	intestine
44	chr1:247373400-247374600	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr1:247373400-247374600	Active TSS	Fetal Stomach	stomach
46	chr1:247373400-247374600	Active TSS	NHEK	skin
47	chr1:247373400-247375600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:247373600-247374400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:247373600-247374400	Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr1:247373600-247374400	Active TSS	Primary T cells from cord blood	blood

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