Variant report

Variant	rs6682353
Chromosome Location	chr1:224033792-224033793
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	CHD2	chr1:224032925-224034617	Hela-S3	cervix:	n/a	chr1:224033803-224033813
2	CTCF	chr1:224033750-224034118	MCF-7	breast:	n/a	chr1:224033881-224033897 chr1:224033882-224033895 chr1:224033882-224033895
3	POLR2A	chr1:224033433-224034227	Raji	blood:	n/a	n/a
4	TBL1XR1	chr1:224033471-224034622	K562	blood:	n/a	n/a
5	CTCF	chr1:224033765-224034067	GM19240	blood:	n/a	chr1:224033881-224033897 chr1:224033882-224033895 chr1:224033882-224033895
6	MAX	chr1:224032986-224034309	K562	blood:	n/a	n/a
7	TAL1	chr1:224033637-224034616	K562	blood:	n/a	n/a
8	TAF1	chr1:224033098-224034370	H1-hESC	embryonic stem cell:	n/a	n/a
9	SP4	chr1:224033659-224034159	H1-hESC	embryonic stem cell:	n/a	n/a
10	EP300	chr1:224033180-224034022	H1-hESC	embryonic stem cell:	n/a	chr1:224033856-224033872 chr1:224033857-224033873 chr1:224033318-224033325 chr1:224033230-224033246
11	CTCF	chr1:224033677-224034131	K562	blood:	n/a	chr1:224033881-224033897 chr1:224033882-224033895 chr1:224033882-224033895
12	NRF1	chr1:224033425-224034135	SK-N-SH	brain:	n/a	chr1:224033767-224033781 chr1:224033767-224033778 chr1:224033769-224033778 chr1:224033764-224033778 chr1:224033767-224033778
13	CTCF	chr1:224033770-224034045	MCF-7	breast:	n/a	chr1:224033881-224033897 chr1:224033882-224033895 chr1:224033882-224033895
14	TCF12	chr1:224032783-224034354	ECC-1	luminal epithelium:	n/a	chr1:224033108-224033118
15	FOS	chr1:224033781-224034010	MCF10A-Er-Src	breast:	n/a	n/a
16	RELA	chr1:224032571-224034424	GM19099	blood:	n/a	chr1:224033222-224033231 chr1:224033222-224033231
17	TAF1	chr1:224033557-224034469	A549	lung:	n/a	n/a
18	MAZ	chr1:224033029-224034297	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:224033225-224034211	HCT-116	colon:	n/a	n/a
20	CEBPB	chr1:224033701-224034248	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr1:224032932-224034356	Hela-S3	cervix:	n/a	n/a
22	NRF1	chr1:224033753-224033853	HepG2	liver:	n/a	chr1:224033767-224033781 chr1:224033767-224033778 chr1:224033769-224033778 chr1:224033764-224033778 chr1:224033767-224033778
23	POLR2A	chr1:224033173-224034286	A549	lung:	n/a	n/a
24	POLR2A	chr1:224033056-224034571	PFSK-1	brain:	n/a	n/a
25	CEBPD	chr1:224033492-224034155	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:224033114-224034559	MCF-7	breast:	n/a	n/a
27	POLR2A	chr1:224033387-224034267	A549	lung:	n/a	n/a
28	EP300	chr1:224032578-224034482	K562	blood:	n/a	chr1:224033856-224033872 chr1:224033857-224033873 chr1:224033318-224033325 chr1:224033230-224033246 chr1:224034068-224034077
29	YY1	chr1:224033690-224034306	HCT-116	colon:	n/a	chr1:224033962-224033973
30	NFIC	chr1:224033782-224034222	HepG2	liver:	n/a	n/a
31	BHLHE40	chr1:224032489-224034345	K562	blood:	n/a	chr1:224033797-224033813 chr1:224033756-224033772
32	POLR2A	chr1:224033133-224034439	HepG2	liver:	n/a	n/a
33	TAF1	chr1:224033542-224034615	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr1:224033114-224034797	Hela-S3	cervix:	n/a	n/a
35	BACH1	chr1:224033703-224033866	H1-hESC	embryonic stem cell:	n/a	n/a
36	YY1	chr1:224033471-224034566	SK-N-SH_RA	brain:	n/a	chr1:224033962-224033973
37	UBTF	chr1:224032527-224034330	K562	blood:	n/a	n/a
38	FOXA1	chr1:224033605-224034034	T-47D	breast:	n/a	n/a
39	POLR2A	chr1:224032904-224034495	HUVEC	blood vessel:	n/a	n/a
40	TAF1	chr1:224033544-224034006	PFSK-1	brain:	n/a	n/a
41	NR3C1	chr1:224033167-224034070	A549	lung:	n/a	n/a
42	HNF4G	chr1:224033205-224034207	HepG2	liver:	n/a	n/a
43	POLR2A	chr1:224031692-224034960	K562	blood:	n/a	n/a
44	YY1	chr1:224033659-224034563	H1-hESC	embryonic stem cell:	n/a	chr1:224033962-224033973
45	POLR2A	chr1:224033584-224034253	PANC-1	pancreas:	n/a	n/a
46	SIN3AK20	chr1:224032887-224034309	SK-N-SH	brain:	n/a	n/a
47	TAF1	chr1:224033754-224034293	Hela-S3	cervix:	n/a	n/a
48	FOSL2	chr1:224033497-224034048	HepG2	liver:	n/a	n/a
49	TAF1	chr1:224033491-224034364	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr1:224033397-224034283	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:223897551..223903480-chr1:224031634..224036730,7	K562	blood:
2	chr1:224008280..224010029-chr1:224031930..224034078,2	MCF-7	breast:
3	chr1:224033539..224034226-chr8:141522052..141522690,2	HCT-116	colon:
4	chr1:223989156..223991507-chr1:224032637..224036039,3	MCF-7	breast:
5	chr1:224033141..224034063-chr17:7747758..7748587,2	Hela-S3	cervix:
6	chr1:223958219..223959890-chr1:224031249..224033872,2	K562	blood:
7	chr1:224031495..224036851-chr1:224037356..224045519,10	MCF-7	breast:
8	chr1:223877159..223879114-chr1:224033630..224035286,2	MCF-7	breast:
9	chr1:223957411..223959662-chr1:224032167..224034658,2	MCF-7	breast:
10	chr1:224001116..224004491-chr1:224031166..224035522,4	K562	blood:
11	chr1:224011114..224014049-chr1:224032766..224036091,4	MCF-7	breast:

Variant related genes	Relation type
TP53BP2	TF binding region
ENSG00000132510	Chromatin interaction
ENSG00000162909	Chromatin interaction
ENSG00000104472	Chromatin interaction
ENSG00000212398	Chromatin interaction
ENSG00000227621	Chromatin interaction
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10915891	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10961	0.84[EUR][1000 genomes]
rs1153948	0.84[EUR][1000 genomes]
rs1415583	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1890120	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2045733	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2126387	0.80[EUR][1000 genomes]
rs3856162	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57453172	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7517814	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7543815	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7547098	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS 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	33 gene(s)	inside rSNPs	diseases
5	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription 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	36 gene(s)	inside rSNPs	diseases
7	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	esv3347515	chr1:224032154-224034902	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr1:224030400-224034400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:224030600-224034600	Active TSS	Aorta	Aorta
3	chr1:224031600-224034200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:224031600-224034200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:224031600-224034400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr1:224031600-224034400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:224031600-224034400	Active TSS	NHLF	lung
8	chr1:224031600-224034600	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr1:224031600-224034800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:224031600-224034800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:224031600-224034800	Active TSS	Right Ventricle	heart
12	chr1:224031800-224034400	Active TSS	H1 Cell Line	embryonic stem cell
13	chr1:224031800-224034400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:224031800-224034400	Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr1:224031800-224034400	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr1:224031800-224034400	Active TSS	Fetal Thymus	thymus
17	chr1:224031800-224034400	Active TSS	Left Ventricle	heart
18	chr1:224031800-224034600	Active TSS	H9 Cell Line	embryonic stem cell
19	chr1:224031800-224034600	Active TSS	Esophagus	oesophagus
20	chr1:224032000-224034200	Active TSS	NH-A	brain
21	chr1:224032000-224034200	Active TSS	NHDF-Ad	bronchial
22	chr1:224032000-224034400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:224032000-224034400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:224032000-224034400	Active TSS	Brain Angular Gyrus	brain
25	chr1:224032000-224034400	Active TSS	Colonic Mucosa	Colon
26	chr1:224032000-224034400	Active TSS	Fetal Intestine Large	intestine
27	chr1:224032000-224034400	Active TSS	Fetal Intestine Small	intestine
28	chr1:224032000-224034400	Active TSS	Fetal Stomach	stomach
29	chr1:224032000-224034400	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr1:224032000-224034400	Active TSS	HSMM	muscle
31	chr1:224032000-224034400	Active TSS	HSMMtube	muscle
32	chr1:224032000-224034600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:224032000-224034600	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr1:224032000-224034600	Active TSS	Brain Substantia Nigra	brain
35	chr1:224032000-224034600	Active TSS	Ovary	ovary
36	chr1:224032000-224034800	Active TSS	Psoas Muscle	Psoas
37	chr1:224032200-224034000	Active TSS	Muscle Satellite Cultured Cells	--
38	chr1:224032200-224034400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:224032200-224034400	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr1:224032200-224034400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:224032200-224034400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:224032200-224034400	Active TSS	Brain Anterior Caudate	brain
43	chr1:224032200-224034400	Active TSS	Brain Cingulate Gyrus	brain
44	chr1:224032200-224034400	Active TSS	Fetal Muscle Trunk	muscle
45	chr1:224032200-224034400	Active TSS	K562	blood
46	chr1:224032200-224034600	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr1:224032200-224034600	Active TSS	Fetal Kidney	kidney
48	chr1:224032200-224034600	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr1:224032200-224034800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr1:224032200-224034800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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