Variant report

Variant	rs7766565
Chromosome Location	chr6:56708693-56708694
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	POLR2A	chr6:56707616-56709245	GM19193	blood:	n/a	n/a
2	POLR2A	chr6:56707687-56709241	MCF-7	breast:	n/a	n/a
3	MAZ	chr6:56707881-56709242	GM12878	blood:	n/a	chr6:56708634-56708644 chr6:56708654-56708663
4	SIN3A	chr6:56707523-56709292	H1-hESC	embryonic stem cell:	n/a	chr6:56708586-56708599 chr6:56708333-56708344
5	PBX3	chr6:56708199-56709320	SK-N-SH	brain:	n/a	n/a
6	FOXM1	chr6:56708688-56709332	GM12878	blood:	n/a	n/a
7	CHD2	chr6:56708689-56709212	H1-hESC	embryonic stem cell:	n/a	n/a
8	RUNX3	chr6:56708610-56709354	GM12878	blood:	n/a	n/a
9	NANOG	chr6:56708599-56709212	H1-hESC	embryonic stem cell:	n/a	n/a
10	MXI1	chr6:56707183-56709485	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr6:56707345-56709348	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr6:56707514-56709185	ProgFib	skin:	n/a	n/a
13	USF1	chr6:56708549-56708774	SK-N-SH_RA	brain:	n/a	chr6:56708610-56708626
14	POLR2A	chr6:56707650-56709132	HEK293	kidney:	n/a	n/a
15	ZBTB7A	chr6:56708521-56709318	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr6:56707320-56709243	H1-neurons	neurons:	n/a	n/a
17	JUND	chr6:56708626-56708854	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr6:56707701-56709206	GM19099	blood:	n/a	n/a
19	RAD21	chr6:56708641-56709463	HCT-116	colon:	n/a	chr6:56709008-56709021
20	POLR2A	chr6:56708010-56709223	MCF-7	breast:	n/a	n/a
21	MAX	chr6:56708669-56709380	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr6:56708636-56709198	U87	brain:	n/a	n/a
23	POLR2A	chr6:56707313-56709296	H1-neurons	neurons:	n/a	n/a
24	POLR2A	chr6:56708625-56709228	HCT-116	colon:	n/a	n/a
25	NFATC1	chr6:56708678-56709328	GM12878	blood:	n/a	n/a
26	TEAD4	chr6:56708317-56709244	SK-N-SH	brain:	n/a	n/a
27	SIN3AK20	chr6:56708601-56709238	SK-N-SH	brain:	n/a	n/a
28	HDAC2	chr6:56708645-56709271	HepG2	liver:	n/a	n/a
29	MXI1	chr6:56707426-56709479	IMR90	lung:	n/a	n/a
30	POLR2A	chr6:56707365-56709352	PANC-1	pancreas:	n/a	n/a
31	ELF1	chr6:56708676-56709210	GM12878	blood:	n/a	n/a
32	HDAC2	chr6:56708668-56709272	MCF-7	breast:	n/a	n/a
33	MAX	chr6:56707899-56709443	A549	lung:	n/a	chr6:56708634-56708644 chr6:56708654-56708663
34	POLR2A	chr6:56708533-56709168	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:56707603-56708700	Gliobla	brain:	n/a	n/a
36	POLR2A	chr6:56708641-56709268	HCT-116	colon:	n/a	n/a
37	TCF12	chr6:56708613-56709330	A549	lung:	n/a	n/a
38	MAX	chr6:56708683-56709223	GM12878	blood:	n/a	n/a
39	HDAC2	chr6:56708586-56709308	H1-hESC	embryonic stem cell:	n/a	n/a
40	TCF3	chr6:56708677-56709183	GM12878	blood:	n/a	n/a
41	TCF12	chr6:56708578-56708944	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr6:56707646-56709262	MCF-7	breast:	n/a	n/a
43	CHD1	chr6:56704985-56709414	IMR90	lung:	n/a	n/a
44	EP300	chr6:56708578-56709253	H1-hESC	embryonic stem cell:	n/a	chr6:56709068-56709084 chr6:56709148-56709164 chr6:56709152-56709168
45	SIN3AK20	chr6:56708680-56709190	PANC-1	pancreas:	n/a	n/a
46	REST	chr6:56707146-56709449	H1-neurons	neurons:	n/a	chr6:56708116-56708129 chr6:56708326-56708344 chr6:56708603-56708616 chr6:56708593-56708603 chr6:56707162-56707171
47	POLR2A	chr6:56708688-56709190	GM12892	blood:	n/a	n/a
48	SIN3AK20	chr6:56708690-56709188	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr6:56707931-56709219	GM10847	blood:	n/a	n/a
50	SP1	chr6:56708580-56709086	H1-hESC	embryonic stem cell:	n/a	chr6:56708634-56708648 chr6:56708633-56708645 chr6:56708633-56708645

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56707257..56710686-chr6:56712186..56717279,8	MCF-7	breast:
2	chr6:56704167..56710132-chr6:56712428..56720773,11	MCF-7	breast:

Variant related genes	Relation type
DST	TF binding region
ENSG00000231441	TF binding region
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10498812	0.89[EUR][1000 genomes]
rs10498813	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13190854	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13192540	0.93[EUR][1000 genomes]
rs13192931	0.93[EUR][1000 genomes]
rs13194625	0.89[EUR][1000 genomes]
rs13194904	0.83[EUR][1000 genomes]
rs13195601	0.90[EUR][1000 genomes]
rs13198204	0.83[EUR][1000 genomes]
rs13198597	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13200166	0.83[EUR][1000 genomes]
rs13200768	0.82[EUR][1000 genomes]
rs13201639	0.83[EUR][1000 genomes]
rs13201733	0.83[EUR][1000 genomes]
rs13203148	0.89[EUR][1000 genomes]
rs13203681	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13204466	0.82[EUR][1000 genomes]
rs13207768	0.95[EUR][1000 genomes]
rs13211879	0.88[EUR][1000 genomes]
rs13214893	0.91[EUR][1000 genomes]
rs13215883	0.93[EUR][1000 genomes]
rs13218913	0.83[EUR][1000 genomes]
rs13220618	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13220628	0.89[EUR][1000 genomes]
rs13220851	0.84[EUR][1000 genomes]
rs1610156	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1610157	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16888171	0.83[EUR][1000 genomes]
rs16888184	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16888186	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17684730	0.83[EUR][1000 genomes]
rs17684748	0.83[EUR][1000 genomes]
rs17684772	0.83[EUR][1000 genomes]
rs17684784	0.83[EUR][1000 genomes]
rs17684802	0.83[EUR][1000 genomes]
rs17684878	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17684884	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17684941	0.92[EUR][1000 genomes]
rs17751966	0.83[EUR][1000 genomes]
rs17751977	0.83[EUR][1000 genomes]
rs17752002	0.83[EUR][1000 genomes]
rs17752046	0.83[EUR][1000 genomes]
rs17752106	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17752213	0.91[EUR][1000 genomes]
rs1903332	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28360570	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34083827	0.90[EUR][1000 genomes]
rs34171958	0.84[EUR][1000 genomes]
rs34228698	0.83[EUR][1000 genomes]
rs34359353	0.84[EUR][1000 genomes]
rs34425815	0.82[EUR][1000 genomes]
rs34520435	0.84[EUR][1000 genomes]
rs34612783	0.82[EUR][1000 genomes]
rs34614087	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34640766	0.83[EUR][1000 genomes]
rs34866877	0.90[EUR][1000 genomes]
rs34896026	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35073881	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35080938	0.94[EUR][1000 genomes]
rs35081015	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35225175	0.89[EUR][1000 genomes]
rs35242294	0.95[EUR][1000 genomes]
rs35251663	0.82[EUR][1000 genomes]
rs35407078	0.90[EUR][1000 genomes]
rs35439100	0.90[EUR][1000 genomes]
rs35440408	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35440822	0.84[EUR][1000 genomes]
rs35461301	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35566812	0.81[EUR][1000 genomes]
rs35609883	0.83[EUR][1000 genomes]
rs35642890	0.83[EUR][1000 genomes]
rs35696739	0.83[EUR][1000 genomes]
rs35828379	0.93[EUR][1000 genomes]
rs35851452	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35873865	0.81[EUR][1000 genomes]
rs35886823	0.83[EUR][1000 genomes]
rs36022925	0.83[EUR][1000 genomes]
rs36037734	0.83[EUR][1000 genomes]
rs36094082	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4299824	0.83[EUR][1000 genomes]
rs4348308	0.83[EUR][1000 genomes]
rs4371846	0.83[EUR][1000 genomes]
rs4415160	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4457154	0.83[EUR][1000 genomes]
rs4532444	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4587171	0.80[EUR][1000 genomes]
rs56037312	0.82[EUR][1000 genomes]
rs59432342	0.83[EUR][1000 genomes]
rs61601344	0.83[EUR][1000 genomes]
rs62411372	0.82[EUR][1000 genomes]
rs62411375	0.82[EUR][1000 genomes]
rs62411376	0.83[EUR][1000 genomes]
rs6905603	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6910414	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6914293	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6918949	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6934714	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71564854	0.83[EUR][1000 genomes]
rs71564855	0.84[EUR][1000 genomes]
rs71564856	0.83[EUR][1000 genomes]
rs71564861	0.83[EUR][1000 genomes]
rs71564863	0.93[EUR][1000 genomes]
rs7758867	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7761501	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7761729	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7771085	0.88[EUR][1000 genomes]
rs7775182	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers 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	28 gene(s)	inside rSNPs	diseases
6	esv3338248	chr6:56707418-56709966	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3350484	chr6:56707493-56709741	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56704000-56709400	Active TSS	Right Atrium	heart
2	chr6:56704200-56709200	Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr6:56704600-56709200	Active TSS	HSMMtube	muscle
4	chr6:56704800-56709400	Active TSS	HSMM	muscle
5	chr6:56705000-56709400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr6:56705200-56709400	Active TSS	Right Ventricle	heart
7	chr6:56705400-56709200	Active TSS	Brain Cingulate Gyrus	brain
8	chr6:56705400-56709200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:56705600-56709200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr6:56705600-56709200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:56705600-56709200	Active TSS	Aorta	Aorta
12	chr6:56705600-56709200	Active TSS	Left Ventricle	heart
13	chr6:56705600-56709200	Active TSS	Stomach Smooth Muscle	stomach
14	chr6:56705600-56709200	Active TSS	NHLF	lung
15	chr6:56705600-56709400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:56705800-56709200	Active TSS	A549	lung
17	chr6:56705800-56709400	Active TSS	Muscle Satellite Cultured Cells	--
18	chr6:56705800-56709400	Active TSS	Brain Anterior Caudate	brain
19	chr6:56706000-56709000	Active TSS	Fetal Brain Female	brain
20	chr6:56706000-56709200	Active TSS	H1 Cell Line	embryonic stem cell
21	chr6:56706000-56709200	Active TSS	Ovary	ovary
22	chr6:56706200-56709200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:56706200-56709200	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr6:56706200-56709200	Active TSS	GM12878-XiMat	blood
25	chr6:56706200-56709400	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr6:56706400-56709200	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr6:56706400-56709200	Active TSS	Brain Angular Gyrus	brain
28	chr6:56706400-56709400	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr6:56706600-56709200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr6:56706800-56709000	Active TSS	NHDF-Ad	bronchial
31	chr6:56706800-56709200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:56706800-56709200	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr6:56706800-56709200	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr6:56706800-56709400	Active TSS	Brain Substantia Nigra	brain
35	chr6:56707000-56708800	Active TSS	NH-A	brain
36	chr6:56707000-56709200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:56707000-56709200	Active TSS	Brain Hippocampus Middle	brain
38	chr6:56707200-56708800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:56707200-56709200	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr6:56707200-56709200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:56707200-56709200	Active TSS	Colon Smooth Muscle	Colon
42	chr6:56707200-56709200	Active TSS	Placenta Amnion	Placenta Amnion
43	chr6:56707200-56709400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:56707400-56709000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:56707400-56709200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:56707400-56709200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:56707400-56709200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:56707400-56709200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:56707400-56709200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:56707400-56709200	Active TSS	Fetal Kidney	kidney

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