Variant report

Variant	rs4615391
Chromosome Location	chr6:53660916-53660917
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	GATA3	chr6:53660389-53661336	MCF-7	breast:	n/a	chr6:53660700-53660708
2	HA-E2F1	chr6:53658249-53661314	MCF-7	breast:	n/a	chr6:53658580-53658592 chr6:53660791-53660806
3	MAX	chr6:53657848-53661452	HCT-116	colon:	n/a	chr6:53660589-53660599
4	SIN3AK20	chr6:53660373-53660946	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZBTB7A	chr6:53659141-53660958	ECC-1	luminal epithelium:	n/a	n/a
6	GATA3	chr6:53660472-53661232	T-47D	breast:	n/a	chr6:53660700-53660708
7	MAX	chr6:53660578-53661305	H1-hESC	embryonic stem cell:	n/a	chr6:53660589-53660599
8	JUN	chr6:53660838-53660927	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAZ	chr6:53658285-53661262	IMR90	lung:	n/a	chr6:53660589-53660599
10	TCF7L2	chr6:53660843-53661533	HEK293	kidney:	n/a	n/a
11	ZEB1	chr6:53657986-53661733	HepG2	liver:	n/a	chr6:53660227-53660234 chr6:53660527-53660534 chr6:53660524-53660535
12	POLR2A	chr6:53660619-53661324	HepG2	liver:	n/a	n/a
13	MAX	chr6:53660606-53661281	ECC-1	luminal epithelium:	n/a	n/a
14	ZBTB7A	chr6:53659259-53660971	ECC-1	luminal epithelium:	n/a	n/a
15	SIN3A	chr6:53658117-53661330	H1-hESC	embryonic stem cell:	n/a	chr6:53658947-53658955 chr6:53660236-53660247
16	MAX	chr6:53660899-53661086	HepG2	liver:	n/a	n/a
17	SIN3AK20	chr6:53660887-53661148	H1-hESC	embryonic stem cell:	n/a	n/a
18	SIN3AK20	chr6:53658042-53661667	MCF-7	breast:	n/a	n/a
19	EGR1	chr6:53658127-53661147	HCT-116	colon:	n/a	chr6:53659819-53659833 chr6:53660784-53660793 chr6:53660781-53660794 chr6:53659793-53659807 chr6:53660041-53660055 chr6:53660781-53660794 chr6:53660783-53660793 chr6:53660781-53660794
20	HEY1	chr6:53660732-53661404	HepG2	liver:	n/a	n/a
21	MYC	chr6:53660810-53661219	MCF10A-Er-Src	breast:	n/a	n/a
22	ZNF143	chr6:53660713-53661172	H1-hESC	embryonic stem cell:	n/a	chr6:53660887-53660905
23	MAX	chr6:53657944-53661423	HepG2	liver:	n/a	chr6:53660589-53660599
24	MAX	chr6:53660542-53661281	H1-hESC	embryonic stem cell:	n/a	chr6:53660589-53660599
25	POLR2A	chr6:53657955-53661480	HepG2	liver:	n/a	n/a
26	POLR2A	chr6:53660783-53660925	MCF-7	breast:	n/a	n/a
27	TCF7L2	chr6:53660680-53661038	PANC-1	pancreas:	n/a	n/a
28	MAX	chr6:53657973-53661406	HCT-116	colon:	n/a	chr6:53660589-53660599
29	CTBP2	chr6:53658435-53661168	H1-hESC	embryonic stem cell:	n/a	n/a
30	ZNF263	chr6:53660548-53661520	HEK293-T-REx	kidney:	n/a	n/a
31	MAX	chr6:53660478-53661404	MCF-7	breast:	n/a	chr6:53660589-53660599
32	ZEB1	chr6:53660554-53661618	HepG2	liver:	n/a	n/a
33	EP300	chr6:53660837-53661000	HepG2	liver:	n/a	n/a
34	MBD4	chr6:53660771-53661312	HepG2	liver:	n/a	n/a
35	NR2F2	chr6:53660324-53661236	MCF-7	breast:	n/a	n/a
36	MAX	chr6:53660299-53661293	MCF-7	breast:	n/a	chr6:53660589-53660599
37	POLR2A	chr6:53660647-53660936	MCF-7	breast:	n/a	n/a
38	SIN3AK20	chr6:53660343-53661350	MCF-7	breast:	n/a	n/a
39	RCOR1	chr6:53658119-53661488	IMR90	lung:	n/a	n/a
40	EGR1	chr6:53660521-53660976	MCF-7	breast:	n/a	chr6:53660784-53660793 chr6:53660781-53660794 chr6:53660781-53660794 chr6:53660783-53660793 chr6:53660781-53660794
41	RCOR1	chr6:53660524-53660974	HepG2	liver:	n/a	n/a
42	GABPA	chr6:53660821-53661448	MCF-7	breast:	n/a	n/a
43	EGR1	chr6:53659091-53661097	HCT-116	colon:	n/a	chr6:53659819-53659833 chr6:53660784-53660793 chr6:53660781-53660794 chr6:53659793-53659807 chr6:53660041-53660055 chr6:53660781-53660794 chr6:53660783-53660793 chr6:53660781-53660794
44	GATA3	chr6:53660332-53661316	MCF-7	breast:	n/a	chr6:53660700-53660708

No.	Distal block	Cell Line	Cell type
1	chr6:53656949..53662173-chr6:53781368..53784554,5	MCF-7	breast:
2	chr6:53660354..53661152-chr6:53734380..53735119,2	MCF-7	breast:
3	chr6:53610265..53615014-chr6:53656858..53662694,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	TF binding region
ENSG00000227885	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10948779	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11755346	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13220665	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2745462	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2820215	0.81[EUR][1000 genomes]
rs2820216	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3000996	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3000997	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3000999	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3001000	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3001001	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3001002	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3001009	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3001010	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3003489	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3003491	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3003493	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3003500	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3003501	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34165049	0.87[EUR][1000 genomes]
rs34861916	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34880762	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35389351	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35517171	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35756855	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3813849	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4236113	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4236115	0.83[AMR][1000 genomes]
rs4265033	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4276502	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4286781	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4321822	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4326237	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4336450	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4351263	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4382260	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4398733	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4437471	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4484515	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4489155	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4591854	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4712048	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4712049	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4715424	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4715426	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59641455	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60035355	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458957	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6458958	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6458959	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6458961	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6458962	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6458965	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6458966	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6458969	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6458971	0.81[EUR][1000 genomes]
rs6458972	0.81[AMR][1000 genomes]
rs6650996	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6899752	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6901644	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6920743	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6924025	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6925836	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6926478	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6937901	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71555560	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7739965	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7753504	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7754791	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7759946	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7762883	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7763081	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7763147	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7769893	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7774173	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9296719	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9296721	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9367544	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9370235	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9370239	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9382234	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9382237	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9382250	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9395886	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv3474747	chr6:53648744-53677210	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3474748	chr6:53648758-53677207	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 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	chr6:53656800-53661200	Active TSS	Fetal Kidney	kidney
2	chr6:53657400-53661200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:53657400-53661400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:53657600-53661000	Active TSS	H1 Cell Line	embryonic stem cell
5	chr6:53657600-53661000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:53657600-53661400	Active TSS	A549	lung
7	chr6:53657800-53661000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:53657800-53661600	Active TSS	Fetal Intestine Large	intestine
9	chr6:53657800-53662400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr6:53658000-53661000	Active TSS	H9 Cell Line	embryonic stem cell
11	chr6:53658000-53661000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:53658000-53661400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:53658000-53661400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:53658000-53661400	Active TSS	Aorta	Aorta
15	chr6:53658000-53661400	Active TSS	Esophagus	oesophagus
16	chr6:53658000-53661600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:53658000-53661600	Active TSS	Fetal Intestine Small	intestine
18	chr6:53658000-53662000	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr6:53658200-53661000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr6:53658200-53661000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:53658200-53661000	Active TSS	Fetal Heart	heart
22	chr6:53658200-53661200	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr6:53658200-53661400	Active TSS	Brain Substantia Nigra	brain
24	chr6:53658200-53661400	Active TSS	Gastric	stomach
25	chr6:53658200-53661400	Active TSS	Ovary	ovary
26	chr6:53658400-53661200	Active TSS	HSMM	muscle
27	chr6:53658400-53661400	Active TSS	Stomach Mucosa	stomach
28	chr6:53658400-53661400	Active TSS	NHLF	lung
29	chr6:53658600-53661000	Active TSS	Brain Angular Gyrus	brain
30	chr6:53658600-53661000	Active TSS	Brain Anterior Caudate	brain
31	chr6:53658600-53661000	Bivalent/Poised TSS	HepG2	liver
32	chr6:53658600-53661800	Active TSS	Brain Hippocampus Middle	brain
33	chr6:53658800-53661000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:53658800-53661000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:53658800-53661000	Active TSS	Small Intestine	intestine
36	chr6:53658800-53661400	Active TSS	Colon Smooth Muscle	Colon
37	chr6:53659000-53661000	Active TSS	Thymus	Thymus
38	chr6:53659000-53661200	Active TSS	Brain Cingulate Gyrus	brain
39	chr6:53659000-53661200	Active TSS	Placenta Amnion	Placenta Amnion
40	chr6:53659000-53661200	Active TSS	NHEK	skin
41	chr6:53659000-53662000	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr6:53659200-53661000	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr6:53659200-53661000	Active TSS	HSMMtube	muscle
44	chr6:53659400-53661000	Active TSS	Fetal Thymus	thymus
45	chr6:53659400-53661000	Active TSS	HMEC	breast
46	chr6:53659800-53661000	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr6:53659800-53661000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:53659800-53661400	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr6:53660000-53661000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr6:53660000-53661000	Flanking Active TSS	Liver	Liver

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