Variant report

Variant	rs12568854
Chromosome Location	chr1:113933570-113933571
allele	A/G/T
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	E2F6	chr1:113933521-113933935	K562	blood:	n/a	n/a
2	HMGN3	chr1:113932545-113934075	K562	blood:	n/a	n/a
3	CTBP2	chr1:113932483-113934232	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr1:113932446-113935004	Hela-S3	cervix:	n/a	chr1:113934693-113934702 chr1:113933283-113933293
5	POLR2A	chr1:113932231-113933669	PFSK-1	brain:	n/a	n/a
6	YY1	chr1:113932507-113933664	HepG2	liver:	n/a	chr1:113933180-113933191 chr1:113932806-113932817 chr1:113933441-113933455 chr1:113933493-113933507 chr1:113933277-113933286 chr1:113933282-113933291
7	ZBTB7A	chr1:113932617-113933735	K562	blood:	n/a	chr1:113933496-113933504 chr1:113933469-113933476 chr1:113933510-113933521
8	MXI1	chr1:113931906-113934933	IMR90	lung:	n/a	n/a
9	ZBTB7A	chr1:113932907-113933883	K562	blood:	n/a	chr1:113933496-113933504 chr1:113933469-113933476 chr1:113933510-113933521
10	UBTF	chr1:113932480-113934161	K562	blood:	n/a	n/a
11	SIN3AK20	chr1:113933060-113933634	PANC-1	pancreas:	n/a	n/a
12	FOXA2	chr1:113933541-113934367	A549	lung:	n/a	n/a
13	MAZ	chr1:113932565-113934246	Hela-S3	cervix:	n/a	chr1:113933283-113933293
14	MAX	chr1:113933544-113934624	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr1:113932419-113933900	MCF10A-Er-Src	breast:	n/a	n/a
16	SMARCB1	chr1:113932526-113934231	Hela-S3	cervix:	n/a	n/a
17	MAX	chr1:113933540-113934257	K562	blood:	n/a	n/a
18	ELF1	chr1:113933388-113934206	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:113932486-113934179	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr1:113933567-113934755	H1-neurons	neurons:	n/a	n/a
21	CCNT2	chr1:113932569-113934081	K562	blood:	n/a	chr1:113933277-113933286
22	ZBTB7A	chr1:113932428-113934336	ECC-1	luminal epithelium:	n/a	chr1:113933496-113933504 chr1:113933469-113933476 chr1:113933510-113933521
23	REST	chr1:113932705-113934744	H1-neurons	neurons:	n/a	chr1:113933450-113933463 chr1:113933434-113933454 chr1:113933434-113933454 chr1:113933146-113933159 chr1:113934569-113934579
24	E2F4	chr1:113932591-113933896	K562	blood:	n/a	chr1:113933298-113933305 chr1:113933297-113933309 chr1:113933274-113933286 chr1:113933298-113933305 chr1:113932753-113932763 chr1:113932969-113932980 chr1:113933228-113933237 chr1:113933298-113933305 chr1:113933277-113933286
25	ZBTB7A	chr1:113932559-113934255	ECC-1	luminal epithelium:	n/a	chr1:113933496-113933504 chr1:113933469-113933476 chr1:113933510-113933521
26	TCF7L2	chr1:113932428-113934536	Hela-S3	cervix:	n/a	n/a
27	SIN3AK20	chr1:113932479-113934680	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr1:113933569-113933631	ProgFib	skin:	n/a	n/a
29	MAZ	chr1:113932524-113933807	GM12878	blood:	n/a	chr1:113933283-113933293
30	ZNF143	chr1:113932468-113933620	GM12878	blood:	n/a	chr1:113932667-113932677 chr1:113933519-113933537 chr1:113933268-113933286
31	POLR2A	chr1:113932463-113934262	K562	blood:	n/a	n/a
32	POLR2A	chr1:113932426-113934224	Hela-S3	cervix:	n/a	n/a
33	RCOR1	chr1:113933448-113934998	IMR90	lung:	n/a	n/a
34	SIN3A	chr1:113931674-113934672	H1-hESC	embryonic stem cell:	n/a	chr1:113933176-113933184 chr1:113933431-113933442
35	MXI1	chr1:113930460-113936450	SK-N-SH	brain:	n/a	n/a
36	MAZ	chr1:113932493-113934510	K562	blood:	n/a	chr1:113933283-113933293
37	NFIC	chr1:113933526-113934060	ECC-1	luminal epithelium:	n/a	n/a
38	HA-E2F1	chr1:113932509-113934478	MCF-7	breast:	n/a	chr1:113933298-113933305 chr1:113933297-113933309 chr1:113934167-113934178 chr1:113933274-113933286 chr1:113933298-113933305 chr1:113932753-113932763 chr1:113933228-113933237 chr1:113933298-113933305 chr1:113933277-113933286
39	SIN3AK20	chr1:113932949-113933575	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr1:113932417-113934088	GM12892	blood:	n/a	n/a
41	CHD2	chr1:113932317-113934694	Hela-S3	cervix:	n/a	chr1:113933275-113933285
42	E2F6	chr1:113932421-113934126	K562	blood:	n/a	chr1:113933298-113933305 chr1:113933297-113933309 chr1:113933274-113933286 chr1:113933298-113933305 chr1:113932753-113932763 chr1:113933228-113933237 chr1:113933298-113933305 chr1:113933277-113933286
43	MAZ	chr1:113931971-113934499	IMR90	lung:	n/a	chr1:113933283-113933293
44	EP300	chr1:113930516-113935379	SK-N-SH	brain:	n/a	chr1:113935085-113935099

No.	Distal block	Cell Line	Cell type
1	chr1:113932997..113933930-chr11:72525071..72525740,2	Hela-S3	cervix:
2	chr1:113931751..113937304-chr1:113991927..113997733,10	MCF-7	breast:
3	chr1:113248698..113251078-chr1:113932422..113935147,2	MCF-7	breast:
4	chr1:113933188..113935605-chr6:26055289..26057331,2	MCF-7	breast:
5	chr1:113932215..113934552-chr4:83350688..83352314,2	MCF-7	breast:
6	chr1:113931908..113934535-chr17:56707476..56709297,2	MCF-7	breast:
7	chr1:113932769..113933633-chr7:91874772..91875450,2	Hela-S3	cervix:
8	chr1:113932898..113933685-chr11:63992576..63993445,2	Hela-S3	cervix:

Variant related genes	Relation type
MAGI3	TF binding region
ENSG00000145293	Chromatin interaction
ENSG00000168010	Chromatin interaction
ENSG00000149761	Chromatin interaction
ENSG00000232499	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000001631	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000149743	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000152795	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10458458	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10458459	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10857994	0.85[ASN][1000 genomes]
rs11102627	0.86[ASN][1000 genomes]
rs11102628	0.86[ASN][1000 genomes]
rs11102630	0.86[ASN][1000 genomes]
rs1112085	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1112543	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12021783	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12023641	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12024428	0.92[ASN][1000 genomes]
rs12029305	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12030900	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12032395	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12034178	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12038879	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12039603	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12048327	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12049093	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12049447	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12567622	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1418607	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1539411	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2027536	0.93[ASN][1000 genomes]
rs2027537	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4839320	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55737954	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66565865	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6688827	0.92[ASN][1000 genomes]
rs72687924	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9787276	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv999873	chr1:113840351-113949453	Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	nsv1010110	chr1:113856612-113969417	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
4	nsv1014757	chr1:113861524-113969417	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113931200-113934400	Active TSS	Rectal Smooth Muscle	rectum
2	chr1:113931200-113935600	Active TSS	NHDF-Ad	bronchial
3	chr1:113931200-113937200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr1:113931400-113934400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr1:113931400-113934800	Active TSS	Gastric	stomach
6	chr1:113931400-113934800	Active TSS	Left Ventricle	heart
7	chr1:113931400-113934800	Active TSS	Pancreas	Pancrea
8	chr1:113931400-113935000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:113931400-113935000	Active TSS	A549	lung
10	chr1:113931600-113934000	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr1:113931600-113934200	Active TSS	Brain Anterior Caudate	brain
12	chr1:113931600-113934400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:113931600-113934800	Active TSS	Right Ventricle	heart
14	chr1:113931600-113934800	Bivalent/Poised TSS	HepG2	liver
15	chr1:113931600-113935000	Active TSS	Stomach Mucosa	stomach
16	chr1:113931600-113935400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:113931600-113935400	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr1:113931600-113935600	Active TSS	Aorta	Aorta
19	chr1:113931600-113935600	Active TSS	Colonic Mucosa	Colon
20	chr1:113931600-113935600	Active TSS	Ovary	ovary
21	chr1:113931600-113936000	Active TSS	Right Atrium	heart
22	chr1:113931600-113937600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:113931800-113933600	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr1:113931800-113934200	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr1:113931800-113934400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr1:113931800-113936000	Active TSS	Colon Smooth Muscle	Colon
27	chr1:113931800-113937400	Active TSS	Fetal Intestine Large	intestine
28	chr1:113932000-113933800	Active TSS	Fetal Muscle Trunk	muscle
29	chr1:113932000-113934000	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr1:113932000-113934200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:113932000-113934400	Active TSS	Placenta Amnion	Placenta Amnion
32	chr1:113932000-113934400	Active TSS	Psoas Muscle	Psoas
33	chr1:113932000-113934600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:113932000-113934800	Active TSS	Esophagus	oesophagus
35	chr1:113932000-113934800	Active TSS	Lung	lung
36	chr1:113932000-113935200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:113932000-113935400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:113932200-113933800	Active TSS	H1 Cell Line	embryonic stem cell
39	chr1:113932200-113933800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:113932200-113934000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:113932200-113934000	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr1:113932200-113934200	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr1:113932200-113934400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:113932200-113934400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:113932200-113934400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:113932200-113934400	Active TSS	NHLF	lung
47	chr1:113932200-113934600	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr1:113932200-113934800	Active TSS	Small Intestine	intestine
49	chr1:113932200-113937200	Active TSS	Fetal Intestine Small	intestine
50	chr1:113932400-113933600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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