Variant report

Variant	rs62400789
Chromosome Location	chr6:24721953-24721954
allele	C/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	EBF1	chr6:24720953-24722332	GM12878	blood:	n/a	n/a
2	REST	chr6:24721531-24722074	PFSK-1	brain:	n/a	n/a
3	TAF1	chr6:24721279-24722164	HepG2	liver:	n/a	n/a
4	KAP1	chr6:24721093-24722265	HEK293	kidney:	n/a	n/a
5	RCOR1	chr6:24720378-24722426	GM12878	blood:	n/a	n/a
6	NFATC1	chr6:24720298-24722239	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:24720466-24722160	HEK293	kidney:	n/a	n/a
8	POLR2A	chr6:24719540-24722490	NB4	blood:	n/a	n/a
9	POLR2A	chr6:24721500-24722147	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAZ	chr6:24719873-24722157	Hela-S3	cervix:	n/a	chr6:24721856-24721863 chr6:24720992-24721002 chr6:24721851-24721866 chr6:24721855-24721864 chr6:24721855-24721864
11	USF2	chr6:24721656-24722012	HepG2	liver:	n/a	n/a
12	RFX5	chr6:24720757-24722225	Hela-S3	cervix:	n/a	chr6:24722201-24722210
13	ZNF384	chr6:24720930-24722053	GM12878	blood:	n/a	n/a
14	IRF4	chr6:24721252-24722221	GM12878	blood:	n/a	n/a
15	CHD2	chr6:24720320-24722058	H1-hESC	embryonic stem cell:	n/a	chr6:24721471-24721481
16	TAF1	chr6:24720417-24722118	ECC-1	luminal epithelium:	n/a	n/a
17	STAT2	chr6:24720844-24722177	K562	blood:	n/a	chr6:24721669-24721680 chr6:24721667-24721682 chr6:24721441-24721448
18	TCF7L2	chr6:24720972-24722127	HCT-116	colon:	n/a	chr6:24721297-24721304
19	MXI1	chr6:24720822-24722108	H1-hESC	embryonic stem cell:	n/a	n/a
20	CEBPD	chr6:24720292-24722191	K562	blood:	n/a	n/a
21	TCF12	chr6:24720535-24722285	A549	lung:	n/a	chr6:24721784-24721791
22	USF1	chr6:24721720-24722008	GM12878	blood:	n/a	n/a
23	BHLHE40	chr6:24721022-24722089	A549	lung:	n/a	chr6:24721097-24721113
24	SMC3	chr6:24720379-24722082	Hela-S3	cervix:	n/a	chr6:24720650-24720660
25	POLR2A	chr6:24720256-24722275	Hela-S3	cervix:	n/a	n/a
26	BHLHE40	chr6:24720460-24722377	K562	blood:	n/a	chr6:24720625-24720641 chr6:24720633-24720649 chr6:24721097-24721113
27	EGR1	chr6:24720878-24721964	K562	blood:	n/a	chr6:24721634-24721647 chr6:24721635-24721649 chr6:24720993-24721003
28	YY1	chr6:24720401-24722056	ECC-1	luminal epithelium:	n/a	chr6:24721092-24721102 chr6:24720994-24721003 chr6:24720789-24720798
29	MYC	chr6:24720900-24722121	Hela-S3	cervix:	n/a	chr6:24721856-24721863 chr6:24720992-24721002 chr6:24721851-24721866 chr6:24721855-24721864 chr6:24721855-24721864
30	POLR2A	chr6:24717288-24722666	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr6:24720241-24722389	SK-N-SH	brain:	n/a	n/a
32	YY1	chr6:24720373-24722142	HepG2	liver:	n/a	chr6:24722106-24722122 chr6:24721092-24721102 chr6:24720994-24721003 chr6:24720789-24720798
33	STAT5A	chr6:24721583-24722169	GM12878	blood:	n/a	chr6:24721669-24721680
34	MYC	chr6:24721342-24722131	HepG2	liver:	n/a	chr6:24721856-24721863 chr6:24721851-24721866 chr6:24721855-24721864 chr6:24721855-24721864
35	CEBPB	chr6:24721176-24722039	A549	lung:	n/a	n/a
36	USF2	chr6:24720555-24722212	GM12878	blood:	n/a	chr6:24720625-24720641 chr6:24720633-24720649 chr6:24721097-24721113
37	TBP	chr6:24720403-24722236	H1-hESC	embryonic stem cell:	n/a	n/a
38	TAF1	chr6:24720348-24722095	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr6:24719329-24722375	ProgFib	skin:	n/a	n/a
40	JUN	chr6:24720841-24722394	K562	blood:	n/a	chr6:24721563-24721574 chr6:24720993-24721002 chr6:24720994-24721003
41	SRF	chr6:24720745-24722103	MCF-7	breast:	n/a	n/a
42	SIX5	chr6:24720839-24722302	A549	lung:	n/a	n/a
43	POLR2A	chr6:24719230-24722689	GM19193	blood:	n/a	n/a
44	STAT1	chr6:24720978-24722125	K562	blood:	n/a	chr6:24721669-24721680 chr6:24721441-24721448
45	POLR2A	chr6:24719246-24722397	GM19099	blood:	n/a	n/a
46	SIN3AK20	chr6:24721359-24722137	HepG2	liver:	n/a	n/a
47	NFYA	chr6:24721055-24722024	Hela-S3	cervix:	n/a	n/a
48	MYC	chr6:24720878-24722173	K562	blood:	n/a	chr6:24721856-24721863 chr6:24720992-24721002 chr6:24721851-24721866 chr6:24721855-24721864 chr6:24721855-24721864
49	MAX	chr6:24720341-24722223	ECC-1	luminal epithelium:	n/a	chr6:24721856-24721863 chr6:24720992-24721002 chr6:24721851-24721866 chr6:24721855-24721864 chr6:24721855-24721864
50	SIN3AK20	chr6:24721463-24722033	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:24711892..24724164-chr6:24769415..24786834,81	K562	blood:
2	chr6:24721486..24723774-chr6:24748539..24750202,2	K562	blood:
3	chr6:24719506..24722494-chr6:24741132..24743826,4	K562	blood:
4	chr6:24721787..24724500-chr6:24751636..24753786,2	MCF-7	breast:
5	chr6:24719119..24721965-chr6:26020764..26023234,2	MCF-7	breast:
6	chr6:24657655..24659922-chr6:24720349..24722391,2	K562	blood:
7	chr6:24715365..24725462-chr6:24770390..24783002,86	K562	blood:
8	chr6:24719711..24722073-chr6:24797818..24801450,3	K562	blood:
9	chr6:24716219..24722234-chr6:24748111..24753033,8	K562	blood:
10	chr17:80186268..80187089-chr6:24721445..24722067,2	HCT-116	colon:
11	chr6:24718870..24722603-chr6:26025035..26028594,6	K562	blood:
12	chr6:24696748..24707740-chr6:24716503..24724189,24	MCF-7	breast:
13	chr5:36241334..36243447-chr6:24720553..24722359,2	K562	blood:
14	chr19:55727413..55728309-chr6:24721650..24722152,2	Hela-S3	cervix:
15	chr6:24493014..24496474-chr6:24718971..24722650,4	K562	blood:
16	chr6:24718549..24722818-chr6:24771512..24777723,8	MCF-7	breast:
17	chr6:24661385..24670379-chr6:24713871..24722680,32	K562	blood:
18	chr6:24720585..24722124-chr7:7679223..7680620,4	Hela-S3	cervix:
19	chr6:24659286..24660892-chr6:24721746..24723397,2	MCF-7	breast:
20	chr6:24717870..24723661-chr6:24773711..24778808,16	MCF-7	breast:
21	chr1:36690058..36690572-chr6:24721190..24722056,2	Hela-S3	cervix:
22	chr18:32821000..32821510-chr6:24721408..24722055,2	Hela-S3	cervix:
23	chr6:24660920..24672880-chr6:24713381..24723000,42	K562	blood:
24	chr6:24720760..24722445-chr6:24809512..24811592,2	K562	blood:
25	chr6:24665745..24668755-chr6:24718443..24722281,4	MCF-7	breast:
26	chr14:53416668..53418435-chr6:24720286..24722655,2	MCF-7	breast:
27	chr6:20401095..20405762-chr6:24718847..24722714,7	K562	blood:
28	chr6:20400126..20404982-chr6:24718144..24722714,11	K562	blood:
29	chr6:24719452..24722494-chr6:24742032..24745228,7	K562	blood:
30	chr6:24492199..24495699-chr6:24718792..24721987,5	K562	blood:

Variant related genes	Relation type
C6orf62	TF binding region
ENSG00000152620	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000260286	Chromatin interaction
ENSG00000141526	Chromatin interaction
ENSG00000112242	Chromatin interaction
ENSG00000111913	Chromatin interaction
ENSG00000073712	Chromatin interaction
ENSG00000112294	Chromatin interaction
ENSG00000224164	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000112293	Chromatin interaction
ENSG00000218806	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000111802	Chromatin interaction
ENSG00000106399	Chromatin interaction
ENSG00000219545	Chromatin interaction
ENSG00000112312	Chromatin interaction
ENSG00000272345	Chromatin interaction
ENSG00000186812	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000272402	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11559067	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16889567	1.00[ASN][1000 genomes]
rs17243276	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17249561	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17249729	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17412874	1.00[ASN][1000 genomes]
rs17419844	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17491730	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212238	1.00[ASN][1000 genomes]
rs62400556	1.00[ASN][1000 genomes]
rs62400558	1.00[ASN][1000 genomes]
rs62400559	1.00[ASN][1000 genomes]
rs62400760	1.00[ASN][1000 genomes]
rs62400773	1.00[ASN][1000 genomes]
rs62400774	1.00[ASN][1000 genomes]
rs62400783	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400786	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400787	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400790	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400791	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62400792	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400793	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400795	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400819	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400821	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62400822	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62402860	1.00[ASN][1000 genomes]
rs62402864	1.00[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	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
4	nsv428474	chr6:24714157-24797977	Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 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	chr6:24716400-24722400	Active TSS	Ovary	ovary
2	chr6:24716600-24722000	Active TSS	Stomach Mucosa	stomach
3	chr6:24716600-24722400	Active TSS	Right Ventricle	heart
4	chr6:24716800-24722400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:24716800-24722600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:24717000-24722200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:24717000-24722400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:24717000-24722400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:24717000-24722400	Active TSS	Brain Angular Gyrus	brain
10	chr6:24717000-24722600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr6:24717400-24722200	Active TSS	Fetal Intestine Large	intestine
12	chr6:24717600-24722000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:24717600-24722200	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr6:24717600-24722200	Active TSS	HSMMtube	muscle
15	chr6:24717800-24722000	Active TSS	Fetal Intestine Small	intestine
16	chr6:24717800-24722000	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr6:24717800-24722000	Active TSS	NHLF	lung
18	chr6:24717800-24722200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:24717800-24722400	Active TSS	H1 Cell Line	embryonic stem cell
20	chr6:24717800-24722400	Active TSS	Psoas Muscle	Psoas
21	chr6:24717800-24722400	Active TSS	Thymus	Thymus
22	chr6:24718000-24722000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr6:24718000-24722200	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr6:24718000-24722400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr6:24718000-24722400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:24718000-24722600	Active TSS	Stomach Smooth Muscle	stomach
27	chr6:24718200-24722000	Active TSS	Placenta	Placenta
28	chr6:24718200-24722200	Active TSS	A549	lung
29	chr6:24718200-24722400	Active TSS	Brain Anterior Caudate	brain
30	chr6:24718400-24722000	Active TSS	Small Intestine	intestine
31	chr6:24718400-24722200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:24718400-24722200	Active TSS	Left Ventricle	heart
33	chr6:24718400-24722200	Active TSS	Lung	lung
34	chr6:24718400-24722200	Active TSS	Placenta Amnion	Placenta Amnion
35	chr6:24718400-24722400	Active TSS	H9 Cell Line	embryonic stem cell
36	chr6:24718600-24722000	Active TSS	Fetal Muscle Trunk	muscle
37	chr6:24718600-24722000	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr6:24718600-24722000	Active TSS	HSMM	muscle
39	chr6:24718600-24722200	Active TSS	Brain Substantia Nigra	brain
40	chr6:24718800-24722000	Active TSS	Pancreas	Pancrea
41	chr6:24718800-24722200	Active TSS	Colonic Mucosa	Colon
42	chr6:24718800-24722600	Active TSS	NHDF-Ad	bronchial
43	chr6:24719000-24722000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:24719000-24722000	Active TSS	Duodenum Mucosa	Duodenum
45	chr6:24719000-24722400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:24719200-24722000	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr6:24719200-24722000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr6:24719200-24722000	Active TSS	Colon Smooth Muscle	Colon
49	chr6:24719200-24722000	Active TSS	Fetal Lung	lung
50	chr6:24719200-24722200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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