Variant report

Variant	rs28555366
Chromosome Location	chr1:242152450-242152451
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	STAT3	chr1:242152419-242152691	MCF10A-Er-Src	breast:	n/a	n/a
2	ZNF263	chr1:242151792-242152970	HEK293-T-REx	kidney:	n/a	chr1:242152767-242152788
3	RFX5	chr1:242152153-242152866	Hela-S3	cervix:	n/a	n/a
4	EP300	chr1:242152186-242152767	Hela-S3	cervix:	n/a	n/a
5	TFAP2C	chr1:242151636-242152784	Hela-S3	cervix:	n/a	n/a
6	MAX	chr1:242152193-242152831	Hela-S3	cervix:	n/a	chr1:242152816-242152825
7	GTF2F1	chr1:242152201-242152668	Hela-S3	cervix:	n/a	n/a
8	NR2F2	chr1:242152090-242152716	MCF-7	breast:	n/a	n/a
9	MEF2A	chr1:242152376-242152679	GM12878	blood:	n/a	n/a
10	STAT3	chr1:242152336-242152858	MCF10A-Er-Src	breast:	n/a	n/a
11	MYC	chr1:242152324-242152839	MCF10A-Er-Src	breast:	n/a	chr1:242152816-242152825
12	SMARCC1	chr1:242151655-242152996	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:242152135-242152486	PANC-1	pancreas:	n/a	n/a
14	STAT3	chr1:242152223-242152854	MCF10A-Er-Src	breast:	n/a	n/a
15	EP300	chr1:242152298-242152806	GM12878	blood:	n/a	n/a
16	TCF12	chr1:242152356-242152737	GM12878	blood:	n/a	chr1:242152528-242152538 chr1:242152529-242152536 chr1:242152494-242152501
17	FOS	chr1:242152189-242152779	MCF10A-Er-Src	breast:	n/a	n/a
18	FOS	chr1:242152381-242152808	MCF10A-Er-Src	breast:	n/a	n/a
19	MAX	chr1:242152185-242152853	Hela-S3	cervix:	n/a	chr1:242152816-242152825
20	TFAP2A	chr1:242151673-242152690	Hela-S3	cervix:	n/a	n/a
21	GATA3	chr1:242152111-242152628	MCF-7	breast:	n/a	n/a
22	SETDB1	chr1:242152375-242152680	U2OS	brain:	n/a	n/a
23	MAFK	chr1:242152163-242152914	Hela-S3	cervix:	n/a	n/a
24	KAP1	chr1:242151638-242152912	HEK293	kidney:	n/a	n/a
25	FOS	chr1:242152126-242152753	Hela-S3	cervix:	n/a	n/a
26	EP300	chr1:242152252-242152520	SK-N-SH_RA	brain:	n/a	n/a
27	CEBPB	chr1:242152115-242152827	Hela-S3	cervix:	n/a	n/a
28	E2F4	chr1:242152409-242152769	MCF10A-Er-Src	breast:	n/a	n/a
29	FOS	chr1:242152151-242152810	MCF10A-Er-Src	breast:	n/a	n/a
30	USF2	chr1:242152306-242152686	Hela-S3	cervix:	n/a	n/a
31	TCF7L2	chr1:242152087-242152524	PANC-1	pancreas:	n/a	n/a
32	FOS	chr1:242152169-242152810	MCF10A-Er-Src	breast:	n/a	n/a
33	RCOR1	chr1:242152233-242152780	Hela-S3	cervix:	n/a	n/a
34	KAP1	chr1:242151694-242153014	U2OS	brain:	n/a	n/a
35	TCF7L2	chr1:242152120-242152781	HEK293	kidney:	n/a	n/a
36	TCF7L2	chr1:242151995-242152683	Hela-S3	cervix:	n/a	n/a
37	RUNX3	chr1:242152439-242152703	GM12878	blood:	n/a	n/a
38	STAT3	chr1:242152244-242152672	Hela-S3	cervix:	n/a	n/a
39	BCL11A	chr1:242152382-242152691	GM12878	blood:	n/a	n/a
40	MEF2A	chr1:242152305-242152775	GM12878	blood:	n/a	n/a
41	STAT3	chr1:242152340-242152778	MCF10A-Er-Src	breast:	n/a	n/a
42	MEF2C	chr1:242152331-242152737	GM12878	blood:	n/a	n/a
43	MYC	chr1:242152310-242152807	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:242144580..242146530-chr1:242152140..242153827,2	K562	blood:
2	chr1:242063761..242065381-chr1:242152078..242153652,2	MCF-7	breast:

Variant related genes	Relation type
CFL1P4	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs2090691	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2090692	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2102911	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28477715	0.82[ASN][1000 genomes]
rs28507487	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28679399	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28693018	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28704168	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28707795	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34947819	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55692832	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55823431	0.82[ASN][1000 genomes]
rs56347031	0.82[ASN][1000 genomes]
rs61844959	0.82[ASN][1000 genomes]
rs61846260	0.82[ASN][1000 genomes]
rs61846264	0.82[ASN][1000 genomes]
rs61846285	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61846287	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72759104	0.82[ASN][1000 genomes]
rs72759106	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72759107	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72759108	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72759110	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72759113	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72759115	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv948409	chr1:241830086-242489705	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1008300	chr1:241886514-242171611	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1008886	chr1:242015591-242176983	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv2750830	chr1:242025098-242303357	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv2750831	chr1:242025098-242332959	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1002309	chr1:242042242-242295635	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	esv3353742	chr1:242129501-242179261	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
10	nsv869647	chr1:242141471-242248271	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv508703	chr1:242146940-242252101	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242121400-242161800	Weak transcription	Right Atrium	heart
2	chr1:242137200-242153200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:242142800-242153400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:242149600-242155600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:242151400-242153600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:242151600-242152600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:242151600-242152600	Enhancers	Adipose Nuclei	Adipose
8	chr1:242151600-242152600	Enhancers	Brain Germinal Matrix	brain
9	chr1:242151600-242153000	Enhancers	Fetal Kidney	kidney
10	chr1:242151600-242153600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:242151600-242153600	Enhancers	Fetal Lung	lung
12	chr1:242151600-242153600	Enhancers	NH-A	brain
13	chr1:242151600-242154400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:242151600-242154400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:242151600-242154400	Enhancers	HSMM	muscle
16	chr1:242151600-242154600	Enhancers	Fetal Muscle Leg	muscle
17	chr1:242151800-242153000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:242152000-242154400	Enhancers	Ovary	ovary
19	chr1:242152000-242156600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:242152200-242152600	Enhancers	Brain Hippocampus Middle	brain
21	chr1:242152200-242153000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:242152200-242153000	Enhancers	HSMMtube	muscle
23	chr1:242152200-242153000	Enhancers	Osteobl	bone
24	chr1:242152200-242154000	Enhancers	A549	lung
25	chr1:242152200-242154200	Enhancers	Muscle Satellite Cultured Cells	--
26	chr1:242152400-242152600	Enhancers	Placenta	Placenta
27	chr1:242152400-242152800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:242152400-242152800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:242152400-242153000	Flanking Active TSS	Hela-S3	cervix
30	chr1:242152400-242153000	Enhancers	NHLF	lung
31	chr1:242152400-242153600	Enhancers	Fetal Stomach	stomach
32	chr1:242152400-242154200	Enhancers	NHDF-Ad	bronchial

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