Variant report

Variant	rs4314499
Chromosome Location	chr6:53660358-53660359
allele	C/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	MAX	chr6:53657995-53660610	ECC-1	luminal epithelium:	n/a	chr6:53660589-53660599
2	MYC	chr6:53660284-53660415	MCF10A-Er-Src	breast:	n/a	n/a
3	CHD2	chr6:53660250-53660368	GM12878	blood:	n/a	n/a
4	HA-E2F1	chr6:53658249-53661314	MCF-7	breast:	n/a	chr6:53658580-53658592 chr6:53660791-53660806
5	MAX	chr6:53657848-53661452	HCT-116	colon:	n/a	chr6:53660589-53660599
6	TBP	chr6:53658870-53660561	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZBTB7A	chr6:53659141-53660958	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr6:53658796-53660424	Hela-S3	cervix:	n/a	n/a
9	SMC3	chr6:53658929-53660419	Hela-S3	cervix:	n/a	n/a
10	MAZ	chr6:53658285-53661262	IMR90	lung:	n/a	chr6:53660589-53660599
11	RFX5	chr6:53660198-53660454	Hela-S3	cervix:	n/a	n/a
12	ZEB1	chr6:53657986-53661733	HepG2	liver:	n/a	chr6:53660227-53660234 chr6:53660527-53660534 chr6:53660524-53660535
13	ZBTB7A	chr6:53659259-53660971	ECC-1	luminal epithelium:	n/a	n/a
14	TAF1	chr6:53659474-53660373	HepG2	liver:	n/a	n/a
15	SIN3A	chr6:53658117-53661330	H1-hESC	embryonic stem cell:	n/a	chr6:53658947-53658955 chr6:53660236-53660247
16	TCF7L2	chr6:53659953-53660435	Hela-S3	cervix:	n/a	n/a
17	SIN3AK20	chr6:53658042-53661667	MCF-7	breast:	n/a	n/a
18	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
19	HCFC1	chr6:53658945-53660683	Hela-S3	cervix:	n/a	n/a
20	MAX	chr6:53658325-53660445	ECC-1	luminal epithelium:	n/a	n/a
21	MAX	chr6:53657944-53661423	HepG2	liver:	n/a	chr6:53660589-53660599
22	POLR2A	chr6:53657955-53661480	HepG2	liver:	n/a	n/a
23	REST	chr6:53659269-53660838	H1-neurons	neurons:	n/a	chr6:53659471-53659484 chr6:53660238-53660256 chr6:53660817-53660830
24	E2F6	chr6:53658239-53660429	H1-hESC	embryonic stem cell:	n/a	chr6:53658580-53658592
25	MAZ	chr6:53659091-53660387	Hela-S3	cervix:	n/a	n/a
26	E2F4	chr6:53660248-53660610	MCF10A-Er-Src	breast:	n/a	n/a
27	SMARCC1	chr6:53659182-53660400	Hela-S3	cervix:	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	SMARCB1	chr6:53658842-53660797	Hela-S3	cervix:	n/a	n/a
31	NR2F2	chr6:53660324-53661236	MCF-7	breast:	n/a	n/a
32	RCOR1	chr6:53658989-53660368	Hela-S3	cervix:	n/a	n/a
33	MAX	chr6:53660299-53661293	MCF-7	breast:	n/a	chr6:53660589-53660599
34	MYC	chr6:53660276-53660589	MCF10A-Er-Src	breast:	n/a	n/a
35	SIN3AK20	chr6:53660343-53661350	MCF-7	breast:	n/a	n/a
36	SIN3A	chr6:53660320-53660482	GM12878	blood:	n/a	n/a
37	CHD1	chr6:53659875-53660520	H1-hESC	embryonic stem cell:	n/a	n/a
38	RCOR1	chr6:53658119-53661488	IMR90	lung:	n/a	n/a
39	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
40	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:
4	chr1:202926993..202927664-chr6:53659752..53660466,2	Hela-S3	cervix:
5	chr17:46125721..46126711-chr6:53659755..53660427,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000228614	TF binding region
ENSG00000227885	Chromatin interaction
ENSG00000159346	Chromatin interaction
ENSG00000137269	Chromatin interaction
ENSG00000082641	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10755766	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1076701	0.84[AMR][1000 genomes]
rs1076702	0.82[AMR][1000 genomes]
rs10948775	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4610551	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6903399	0.93[AMR][1000 genomes]
rs6921605	0.88[AMR][1000 genomes]
rs9349685	0.84[AMR][1000 genomes]
rs9357776	0.81[AMR][1000 genomes]
rs9370233	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9382231	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9382232	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9382233	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9382235	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9382238	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9382241	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9382243	0.90[AMR][1000 genomes]
rs9382244	0.90[AMR][1000 genomes]
rs9382246	0.90[AMR][1000 genomes]
rs9382248	0.86[AMR][1000 genomes]
rs9382253	0.82[AMR][1000 genomes]
rs9382254	0.82[AMR][1000 genomes]
rs9382257	0.82[AMR][1000 genomes]
rs9395876	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9395878	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9395881	0.88[AMR][1000 genomes]
rs9474649	0.87[AMR][1000 genomes];0.84[ASN][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:126 , 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	chr6:53658000-53660400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:53658000-53660400	Active TSS	Rectal Smooth Muscle	rectum
12	chr6:53658000-53660600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:53658000-53660600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:53658000-53660600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:53658000-53660800	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr6:53658000-53661000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr6:53658000-53661000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:53658000-53661400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:53658000-53661400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:53658000-53661400	Active TSS	Aorta	Aorta
21	chr6:53658000-53661400	Active TSS	Esophagus	oesophagus
22	chr6:53658000-53661600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:53658000-53661600	Active TSS	Fetal Intestine Small	intestine
24	chr6:53658000-53662000	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr6:53658200-53660400	Active TSS	Left Ventricle	heart
26	chr6:53658200-53660400	Active TSS	Pancreas	Pancrea
27	chr6:53658200-53660600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:53658200-53660800	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr6:53658200-53660800	Active TSS	Right Atrium	heart
30	chr6:53658200-53661000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr6:53658200-53661000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:53658200-53661000	Active TSS	Fetal Heart	heart
33	chr6:53658200-53661200	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr6:53658200-53661400	Active TSS	Brain Substantia Nigra	brain
35	chr6:53658200-53661400	Active TSS	Gastric	stomach
36	chr6:53658200-53661400	Active TSS	Ovary	ovary
37	chr6:53658400-53661200	Active TSS	HSMM	muscle
38	chr6:53658400-53661400	Active TSS	Stomach Mucosa	stomach
39	chr6:53658400-53661400	Active TSS	NHLF	lung
40	chr6:53658600-53660600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:53658600-53660800	Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr6:53658600-53661000	Active TSS	Brain Angular Gyrus	brain
43	chr6:53658600-53661000	Active TSS	Brain Anterior Caudate	brain
44	chr6:53658600-53661000	Bivalent/Poised TSS	HepG2	liver
45	chr6:53658600-53661800	Active TSS	Brain Hippocampus Middle	brain
46	chr6:53658800-53660400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:53658800-53661000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:53658800-53661000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:53658800-53661000	Active TSS	Small Intestine	intestine
50	chr6:53658800-53661400	Active TSS	Colon Smooth Muscle	Colon

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