Variant report

Variant	rs73412140
Chromosome Location	chr6:33757014-33757015
allele	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	EGR1	chr6:33756776-33757313	ECC-1	luminal epithelium:	n/a	n/a
2	CREB1	chr6:33756523-33757343	H1-hESC	embryonic stem cell:	n/a	n/a
3	CREB1	chr6:33756550-33757443	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:33755871-33757080	K562	blood:	n/a	n/a
5	YY1	chr6:33755711-33757699	SK-N-SH	brain:	n/a	chr6:33757002-33757014 chr6:33756132-33756143 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
6	TCF12	chr6:33755925-33757295	ECC-1	luminal epithelium:	n/a	n/a
7	TCF12	chr6:33756818-33757126	HepG2	liver:	n/a	n/a
8	USF1	chr6:33756873-33757099	SK-N-SH_RA	brain:	n/a	n/a
9	MAZ	chr6:33754791-33757409	IMR90	lung:	n/a	chr6:33756978-33756987
10	POLR2A	chr6:33756674-33757097	K562	blood:	n/a	n/a
11	PML	chr6:33756582-33757228	MCF-7	breast:	n/a	n/a
12	ELF1	chr6:33756691-33757148	SK-N-SH	brain:	n/a	n/a
13	CHD1	chr6:33753489-33757327	IMR90	lung:	n/a	n/a
14	POLR2A	chr6:33754637-33757242	SK-N-MC	brain:	n/a	n/a
15	MYC	chr6:33756860-33757286	H1-hESC	embryonic stem cell:	n/a	chr6:33756978-33756987
16	SP4	chr6:33756707-33757298	H1-hESC	embryonic stem cell:	n/a	chr6:33756966-33756982
17	POLR2A	chr6:33755375-33757546	GM12878	blood:	n/a	n/a
18	MXI1	chr6:33756744-33757150	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZNF143	chr6:33756738-33757128	Hela-S3	cervix:	n/a	n/a
20	THAP1	chr6:33756530-33757096	K562	blood:	n/a	n/a
21	CREB1	chr6:33756488-33757323	GM12878	blood:	n/a	n/a
22	ATF2	chr6:33756884-33757231	GM12878	blood:	n/a	n/a
23	EGR1	chr6:33756761-33757355	MCF-7	breast:	n/a	n/a
24	POLR2A	chr6:33755402-33757555	GM12892	blood:	n/a	n/a
25	MBD4	chr6:33756740-33757266	HepG2	liver:	n/a	n/a
26	ETS1	chr6:33756513-33757346	K562	blood:	n/a	chr6:33756967-33756978
27	RCOR1	chr6:33756773-33757212	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr6:33756661-33757220	HepG2	liver:	n/a	n/a
29	POLR2A	chr6:33755726-33757121	HepG2	liver:	n/a	n/a
30	PML	chr6:33756641-33757241	K562	blood:	n/a	n/a
31	SIX5	chr6:33756771-33757239	K562	blood:	n/a	n/a
32	TAF7	chr6:33756373-33757221	H1-hESC	embryonic stem cell:	n/a	n/a
33	TAF1	chr6:33756487-33757099	H1-hESC	embryonic stem cell:	n/a	n/a
34	TAF1	chr6:33756645-33757097	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr6:33756714-33757263	U87	brain:	n/a	n/a
36	MXI1	chr6:33756653-33757100	K562	blood:	n/a	n/a
37	TBP	chr6:33756688-33757175	HepG2	liver:	n/a	n/a
38	RELA	chr6:33756704-33757259	GM15510	blood:	n/a	n/a
39	ETS1	chr6:33756703-33757221	GM12878	blood:	n/a	chr6:33756967-33756978
40	CBX3	chr6:33756675-33757498	K562	blood:	n/a	n/a
41	YY1	chr6:33756654-33757183	K562	blood:	n/a	chr6:33757002-33757014 chr6:33757003-33757013 chr6:33757003-33757025 chr6:33756966-33756980 chr6:33757006-33757014 chr6:33757002-33757018
42	STAT5A	chr6:33756444-33757168	GM12878	blood:	n/a	n/a
43	GABPA	chr6:33756538-33757090	HepG2	liver:	n/a	chr6:33756969-33756978 chr6:33756952-33756966
44	TRIM28	chr6:33756698-33757299	K562	blood:	n/a	n/a
45	TAF1	chr6:33756491-33757219	PFSK-1	brain:	n/a	n/a
46	POLR2A	chr6:33755608-33757706	HL-60	blood:	n/a	n/a
47	CEBPB	chr6:33756846-33757373	K562	blood:	n/a	n/a
48	EP300	chr6:33756730-33757119	SK-N-SH_RA	brain:	n/a	chr6:33756943-33756959
49	CUX1	chr6:33756831-33757266	GM12878	blood:	n/a	n/a
50	POLR2A	chr6:33754123-33757999	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33677680..33679812-chr6:33755384..33758328,2	MCF-7	breast:
2	chr6:33677771..33685795-chr6:33753004..33758704,10	MCF-7	breast:
3	chr6:33755468..33757115-chr6:34205033..34207556,2	MCF-7	breast:
4	chr6:33754851..33757425-chr6:33862551..33864997,3	MCF-7	breast:
5	chr6:33756927..33758602-chr6:33764987..33767346,2	MCF-7	breast:
6	chr6:33678014..33680671-chr6:33755515..33757218,2	K562	blood:

Variant related genes	Relation type
LEMD2	TF binding region
ENSG00000137288	Chromatin interaction
ENSG00000137309	Chromatin interaction
ENSG00000249346	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1075379	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11753083	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754690	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11755593	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11757524	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11758463	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12524768	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12524835	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1887340	0.94[EUR][1000 genomes]
rs2281819	0.89[EUR][1000 genomes]
rs2395400	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2894342	0.89[EUR][1000 genomes]
rs3763253	0.89[EUR][1000 genomes]
rs3828783	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4711346	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55775340	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59137082	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61394483	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61662306	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6910736	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6921487	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6930201	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6933174	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933568	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6933607	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6940353	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72880511	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73746509	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs747692	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs751096	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs755495	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7755323	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs943461	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs943462	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs943466	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers 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	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	esv3436027	chr6:33754374-33758772	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33755600-33757200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:33755600-33757400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr6:33755800-33757200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:33755800-33757200	Active TSS	H9 Cell Line	embryonic stem cell
5	chr6:33755800-33757200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:33755800-33757200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:33755800-33757200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:33755800-33757200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:33755800-33757200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:33755800-33757200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:33755800-33757200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:33755800-33757200	Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr6:33755800-33757200	Active TSS	Fetal Intestine Large	intestine
14	chr6:33755800-33757200	Active TSS	Fetal Intestine Small	intestine
15	chr6:33755800-33757200	Active TSS	Left Ventricle	heart
16	chr6:33755800-33757200	Active TSS	Lung	lung
17	chr6:33755800-33757200	Active TSS	Thymus	Thymus
18	chr6:33755800-33757200	Active TSS	A549	lung
19	chr6:33755800-33757200	Active TSS	GM12878-XiMat	blood
20	chr6:33755800-33757200	Active TSS	HSMM	muscle
21	chr6:33755800-33757200	Active TSS	HSMMtube	muscle
22	chr6:33755800-33757200	Active TSS	NH-A	brain
23	chr6:33755800-33757200	Active TSS	NHDF-Ad	bronchial
24	chr6:33755800-33757400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:33755800-33757400	Active TSS	Gastric	stomach
26	chr6:33755800-33757400	Active TSS	Psoas Muscle	Psoas
27	chr6:33755800-33757600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr6:33756000-33757200	Active TSS	H1 Cell Line	embryonic stem cell
29	chr6:33756000-33757200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:33756000-33757200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:33756000-33757200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:33756000-33757200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:33756000-33757200	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr6:33756000-33757200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:33756000-33757200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:33756000-33757200	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr6:33756000-33757200	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr6:33756000-33757200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr6:33756000-33757200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:33756000-33757200	Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr6:33756000-33757200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:33756000-33757200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr6:33756000-33757200	Active TSS	Muscle Satellite Cultured Cells	--
44	chr6:33756000-33757200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:33756000-33757200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:33756000-33757200	Active TSS	Liver	Liver
47	chr6:33756000-33757200	Active TSS	Brain Angular Gyrus	brain
48	chr6:33756000-33757200	Active TSS	Brain Anterior Caudate	brain
49	chr6:33756000-33757200	Active TSS	Brain Cingulate Gyrus	brain
50	chr6:33756000-33757200	Active TSS	Brain Hippocampus Middle	brain

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