Variant report

Variant	rs4653877
Chromosome Location	chr1:223843190-223843191
allele	C/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	NR3C1	chr1:223842789-223843412	A549	lung:	n/a	n/a
2	GATA3	chr1:223842543-223843433	MCF-7	breast:	n/a	n/a
3	HDAC2	chr1:223842752-223843375	MCF-7	breast:	n/a	chr1:223843217-223843231 chr1:223843214-223843228 chr1:223843213-223843227 chr1:223843209-223843223 chr1:223843218-223843232
4	FOSL2	chr1:223842804-223843319	A549	lung:	n/a	n/a
5	FOS	chr1:223842902-223843256	Hela-S3	cervix:	n/a	n/a
6	FOSL2	chr1:223842737-223843397	MCF-7	breast:	n/a	n/a
7	FOSL2	chr1:223842694-223843332	MCF-7	breast:	n/a	n/a
8	POLR2A	chr1:223842925-223843234	HCT-116	colon:	n/a	n/a
9	BCL3	chr1:223842759-223843334	A549	lung:	n/a	n/a
10	NR2F2	chr1:223842523-223843466	MCF-7	breast:	n/a	n/a
11	JUND	chr1:223842948-223843256	HepG2	liver:	n/a	n/a
12	GATA3	chr1:223842748-223843270	MCF-7	breast:	n/a	n/a
13	MAX	chr1:223842530-223843811	A549	lung:	n/a	n/a
14	EP300	chr1:223842656-223843416	MCF-7	breast:	n/a	chr1:223843092-223843099 chr1:223843214-223843228
15	POLR2A	chr1:223842924-223843250	PANC-1	pancreas:	n/a	n/a
16	GATA3	chr1:223842878-223843245	T-47D	breast:	n/a	n/a
17	MAX	chr1:223842547-223843310	MCF-7	breast:	n/a	n/a
18	CEBPB	chr1:223842598-223843268	MCF-7	breast:	n/a	n/a
19	FOXM1	chr1:223842687-223843374	MCF-7	breast:	n/a	n/a
20	ZNF217	chr1:223842618-223843406	MCF-7	breast:	n/a	n/a
21	FOXA2	chr1:223842976-223843226	HepG2	liver:	n/a	n/a
22	TCF7L2	chr1:223842675-223843304	MCF-7	breast:	n/a	chr1:223843167-223843174 chr1:223843163-223843179 chr1:223843166-223843175 chr1:223843163-223843179
23	TCF7L2	chr1:223842868-223843198	PANC-1	pancreas:	n/a	chr1:223843167-223843174 chr1:223843163-223843179 chr1:223843166-223843175 chr1:223843163-223843179
24	EP300	chr1:223842683-223843350	MCF-7	breast:	n/a	chr1:223843092-223843099 chr1:223843214-223843228
25	GATA3	chr1:223842794-223843369	A549	lung:	n/a	n/a
26	USF2	chr1:223842860-223843200	Hela-S3	cervix:	n/a	n/a
27	NR3C1	chr1:223842972-223843201	A549	lung:	n/a	n/a
28	FOXA1	chr1:223842964-223843329	T-47D	breast:	n/a	n/a
29	MAX	chr1:223842684-223843355	MCF-7	breast:	n/a	n/a
30	SIN3AK20	chr1:223842568-223843476	MCF-7	breast:	n/a	n/a
31	TCF12	chr1:223842770-223843439	A549	lung:	n/a	n/a
32	MYC	chr1:223842887-223843191	MCF-7	breast:	n/a	n/a
33	GATA2	chr1:223842889-223843212	SH-SY5Y	brain:	n/a	n/a
34	SP1	chr1:223842686-223843423	A549	lung:	n/a	n/a
35	USF1	chr1:223842938-223843296	A549	lung:	n/a	n/a
36	GATA3	chr1:223842702-223843360	MCF-7	breast:	n/a	n/a
37	FOXA2	chr1:223842594-223843478	A549	lung:	n/a	n/a
38	STAT3	chr1:223842856-223843233	MCF10A-Er-Src	breast:	n/a	n/a
39	GATA3	chr1:223842580-223843560	A549	lung:	n/a	n/a
40	TCF12	chr1:223842550-223843302	MCF-7	breast:	n/a	n/a
41	SIN3AK20	chr1:223842505-223843576	MCF-7	breast:	n/a	n/a
42	ESR1	chr1:223842892-223843240	T-47D	breast:	n/a	chr1:223843083-223843098 chr1:223843083-223843100
43	JUND	chr1:223842876-223843245	A549	lung:	n/a	n/a
44	FOXA1	chr1:223842956-223843279	HepG2	liver:	n/a	n/a
45	FOS	chr1:223842911-223843289	MCF10A-Er-Src	breast:	n/a	n/a
46	GATA2	chr1:223842878-223843206	HUVEC	blood vessel:	n/a	n/a
47	FOSL1	chr1:223842793-223843441	HCT-116	colon:	n/a	n/a
48	TEAD4	chr1:223842830-223843337	A549	lung:	n/a	n/a
49	FOXM1	chr1:223842700-223843369	MCF-7	breast:	n/a	n/a
50	FOS	chr1:223842800-223843319	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:223843142..223845522-chr1:223848017..223849601,2	K562	blood:
2	chr1:223840282..223843675-chr1:223851675..223856291,7	MCF-7	breast:
3	chr1:223842591..223843487-chr1:223870928..223871712,2	MCF-7	breast:
4	chr1:223322225..223323066-chr1:223842691..223843630,2	MCF-7	breast:
5	chr1:223836208..223847031-chr1:223849408..223858826,22	MCF-7	breast:

Variant related genes	Relation type
CAPN8	TF binding region
ENSG00000203697	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10495210	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10495212	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10799570	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915972	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916633	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1109222	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1125346	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12408619	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12566877	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2186009	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34089008	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653518	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4653523	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4653859	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4653863	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4653868	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4653870	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57611697	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60773808	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61825220	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6661481	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6671050	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6677146	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687391	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6687688	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6691383	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6693911	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6701150	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68072917	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72629690	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72629691	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[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	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv873209	chr1:223707647-223846564	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv873210	chr1:223707647-223856414	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv873211	chr1:223707647-223867631	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1000199	chr1:223803545-223854859	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv873212	chr1:223807262-223853792	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1012050	chr1:223824652-223843610	Weak transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv535309	chr1:223824652-223843610	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223833600-223850800	Weak transcription	Colonic Mucosa	Colon
2	chr1:223838200-223850800	Weak transcription	Fetal Stomach	stomach
3	chr1:223839200-223843600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:223840000-223843600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:223840600-223843400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:223840600-223853200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:223840800-223843400	Enhancers	NHEK	skin
8	chr1:223840800-223843600	Enhancers	Stomach Mucosa	stomach
9	chr1:223841000-223843800	Enhancers	HMEC	breast
10	chr1:223841600-223843800	Enhancers	Duodenum Mucosa	Duodenum
11	chr1:223841600-223843800	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr1:223841800-223843400	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr1:223841800-223843800	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr1:223842000-223843600	Enhancers	Gastric	stomach
15	chr1:223842600-223843200	Enhancers	Liver	Liver
16	chr1:223842600-223843600	Flanking Active TSS	A549	lung
17	chr1:223842600-223843600	Enhancers	HepG2	liver
18	chr1:223842600-223843800	Enhancers	Hela-S3	cervix
19	chr1:223843000-223843200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr1:223843000-223843600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:223843000-223843600	Enhancers	Fetal Intestine Large	intestine

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