Variant report

Variant	rs2754775
Chromosome Location	chr6:24775181-24775182
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	USF2	chr6:24774762-24775830	GM12878	blood:	n/a	chr6:24775171-24775182
2	NRF1	chr6:24774944-24775251	HepG2	liver:	n/a	chr6:24775090-24775099 chr6:24775090-24775104 chr6:24775090-24775101 chr6:24775089-24775100 chr6:24775087-24775101
3	STAT5A	chr6:24775103-24775521	GM12878	blood:	n/a	n/a
4	ZNF143	chr6:24774868-24776088	K562	blood:	n/a	n/a
5	POLR2A	chr6:24774855-24776130	MCF10A-Er-Src	breast:	n/a	n/a
6	ELF1	chr6:24774765-24775802	K562	blood:	n/a	chr6:24775574-24775585
7	POLR2A	chr6:24774792-24775917	SK-N-SH	brain:	n/a	n/a
8	MYC	chr6:24774647-24775943	NB4	blood:	n/a	n/a
9	ZC3H11A	chr6:24774810-24775441	K562	blood:	n/a	n/a
10	ETS1	chr6:24775033-24775559	K562	blood:	n/a	chr6:24775360-24775371 chr6:24775359-24775373 chr6:24775359-24775370 chr6:24775099-24775113 chr6:24775358-24775371
11	CTCF	chr6:24775100-24775393	T-47D	breast:	n/a	n/a
12	POLR2A	chr6:24774650-24775908	HCT-116	colon:	n/a	n/a
13	POLR2A	chr6:24774851-24776162	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr6:24774693-24777046	GM12892	blood:	n/a	n/a
15	POLR2A	chr6:24774883-24775974	ECC-1	luminal epithelium:	n/a	n/a
16	TAF1	chr6:24774888-24775892	K562	blood:	n/a	n/a
17	REST	chr6:24775122-24775526	A549	lung:	n/a	n/a
18	POU2F2	chr6:24775125-24775340	GM12878	blood:	n/a	n/a
19	FOXP2	chr6:24774995-24775817	PFSK-1	brain:	n/a	n/a
20	HNF4A	chr6:24774774-24775231	HepG2	liver:	n/a	chr6:24775019-24775034 chr6:24775020-24775032 chr6:24775019-24775033 chr6:24775020-24775032 chr6:24775019-24775032 chr6:24775020-24775033 chr6:24775019-24775033 chr6:24775017-24775035 chr6:24775015-24775037 chr6:24775020-24775032 chr6:24775019-24775034 chr6:24775019-24775033 chr6:24775018-24775033
21	MAX	chr6:24774784-24775841	ECC-1	luminal epithelium:	n/a	n/a
22	YY1	chr6:24774970-24775869	HepG2	liver:	n/a	n/a
23	MXI1	chr6:24774835-24776290	GM12878	blood:	n/a	n/a
24	CREB1	chr6:24774747-24776302	HepG2	liver:	n/a	n/a
25	POLR2A	chr6:24774810-24776017	MCF-7	breast:	n/a	n/a
26	MXI1	chr6:24774576-24776421	IMR90	lung:	n/a	n/a
27	HNF4G	chr6:24774827-24775581	HepG2	liver:	n/a	chr6:24775019-24775034 chr6:24775020-24775032 chr6:24775019-24775033 chr6:24775020-24775032 chr6:24775019-24775032 chr6:24775020-24775033 chr6:24775019-24775033 chr6:24775017-24775035 chr6:24775015-24775037 chr6:24775020-24775032 chr6:24775019-24775034 chr6:24775019-24775033
28	POLR2A	chr6:24774765-24776298	GM18505	blood:	n/a	n/a
29	POLR2A	chr6:24774570-24776016	HL-60	blood:	n/a	n/a
30	TAF1	chr6:24775021-24775885	GM12892	blood:	n/a	n/a
31	HA-E2F1	chr6:24775040-24775929	Hela-S3	cervix:	n/a	chr6:24775561-24775572 chr6:24775560-24775571 chr6:24775561-24775569 chr6:24775561-24775569 chr6:24775560-24775570 chr6:24775659-24775668 chr6:24775561-24775568 chr6:24775558-24775575 chr6:24775091-24775100 chr6:24775562-24775576
32	POLR2A	chr6:24774819-24775933	SK-N-MC	brain:	n/a	n/a
33	NFYB	chr6:24775020-24776035	K562	blood:	n/a	chr6:24775584-24775599 chr6:24775585-24775599 chr6:24775543-24775553 chr6:24775584-24775599 chr6:24775542-24775557 chr6:24775586-24775601
34	POLR2A	chr6:24774763-24776287	K562	blood:	n/a	n/a
35	SIN3A	chr6:24774602-24776180	H1-hESC	embryonic stem cell:	n/a	chr6:24775672-24775681
36	USF2	chr6:24774697-24776186	H1-hESC	embryonic stem cell:	n/a	chr6:24775171-24775182
37	ZEB1	chr6:24775050-24775336	GM12878	blood:	n/a	n/a
38	USF1	chr6:24774922-24775407	A549	lung:	n/a	n/a
39	SIN3AK20	chr6:24774898-24776008	PANC-1	pancreas:	n/a	n/a
40	MXI1	chr6:24774753-24776160	HepG2	liver:	n/a	n/a
41	MAZ	chr6:24774893-24776061	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:24774943-24775833	A549	lung:	n/a	n/a
43	MAZ	chr6:24774882-24776079	HepG2	liver:	n/a	n/a
44	POU2F2	chr6:24774916-24775555	GM12891	blood:	n/a	chr6:24775504-24775516
45	POLR2A	chr6:24775030-24775874	HepG2	liver:	n/a	n/a
46	ELF1	chr6:24774897-24775910	MCF-7	breast:	n/a	chr6:24775574-24775585
47	MYC	chr6:24774628-24776194	K562	blood:	n/a	n/a
48	POLR2A	chr6:24774767-24776156	PANC-1	pancreas:	n/a	n/a
49	CREB1	chr6:24774834-24776079	K562	blood:	n/a	n/a
50	BCLAF1	chr6:24774660-24775889	GM12878	blood:	n/a	chr6:24775359-24775368 chr6:24775456-24775469 chr6:24775571-24775580

No.	Distal block	Cell Line	Cell type
1	chr6:24706431..24709046-chr6:24773872..24777096,3	K562	blood:
2	chr6:24718549..24722818-chr6:24771512..24777723,8	MCF-7	breast:
3	chr6:24774752..24775406-chr7:100486913..100487602,2	HCT-116	colon:
4	chr6:24666490..24670247-chr6:24774150..24780460,9	K562	blood:
5	chr6:24711892..24724164-chr6:24769415..24786834,81	K562	blood:
6	chr6:24493803..24496211-chr6:24773975..24776646,3	K562	blood:
7	chr6:24522066..24523918-chr6:24775174..24778168,2	K562	blood:
8	chr17:7482194..7483174-chr6:24774784..24775711,2	NB4	blood:
9	chr6:24715365..24725462-chr6:24770390..24783002,86	K562	blood:
10	chr6:24717870..24723661-chr6:24773711..24778808,16	MCF-7	breast:
11	chr6:24665480..24670247-chr6:24773496..24779775,9	K562	blood:
12	chr6:24705180..24707870-chr6:24773614..24775393,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACOT13-2	chr6:24775177-24775340	NONHSAT108124

Variant related genes	Relation type
GMNN	TF binding region
ENSG00000176125	Chromatin interaction
ENSG00000272402	Chromatin interaction
ENSG00000112293	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000111802	Chromatin interaction
ENSG00000129226	Chromatin interaction
ENSG00000112294	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1980643	1.00[JPT][hapmap]
rs2245409	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475149	0.84[ASN][1000 genomes]
rs2817735	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv5227	chr6:24774149-24824012	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking 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 miRNA target site	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	chr6:24774200-24776000	Active TSS	Duodenum Mucosa	Duodenum
2	chr6:24774200-24776600	Active TSS	Fetal Brain Female	brain
3	chr6:24774200-24777000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:24774200-24778200	Active TSS	K562	blood
5	chr6:24774400-24775600	Active TSS	Primary T cells fromperipheralblood	blood
6	chr6:24774400-24776000	Active TSS	Fetal Muscle Trunk	muscle
7	chr6:24774400-24776000	Active TSS	Placenta	Placenta
8	chr6:24774400-24776400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:24774400-24776400	Active TSS	Fetal Intestine Large	intestine
10	chr6:24774400-24776400	Active TSS	Placenta Amnion	Placenta Amnion
11	chr6:24774400-24776400	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr6:24774400-24776400	Active TSS	Stomach Smooth Muscle	stomach
13	chr6:24774400-24776600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:24774400-24776600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:24774400-24776600	Active TSS	Fetal Intestine Small	intestine
16	chr6:24774400-24776600	Active TSS	Thymus	Thymus
17	chr6:24774400-24776800	Active TSS	Brain Hippocampus Middle	brain
18	chr6:24774400-24776800	Active TSS	Colonic Mucosa	Colon
19	chr6:24774400-24777000	Active TSS	Brain Germinal Matrix	brain
20	chr6:24774400-24777200	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr6:24774400-24778400	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr6:24774600-24775200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:24774600-24775200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr6:24774600-24775200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:24774600-24775200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:24774600-24775200	Active TSS	Fetal Brain Male	brain
27	chr6:24774600-24775600	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr6:24774600-24775800	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr6:24774600-24775800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:24774600-24775800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr6:24774600-24775800	Active TSS	Adipose Nuclei	Adipose
32	chr6:24774600-24776000	Active TSS	Brain Cingulate Gyrus	brain
33	chr6:24774600-24776000	Active TSS	Brain Substantia Nigra	brain
34	chr6:24774600-24776000	Active TSS	Fetal Muscle Leg	muscle
35	chr6:24774600-24776200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:24774600-24776200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:24774600-24776200	Active TSS	Aorta	Aorta
38	chr6:24774600-24776200	Active TSS	Colon Smooth Muscle	Colon
39	chr6:24774600-24776200	Active TSS	Psoas Muscle	Psoas
40	chr6:24774600-24776400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:24774600-24776400	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr6:24774600-24776400	Active TSS	Esophagus	oesophagus
43	chr6:24774600-24776400	Active TSS	Fetal Lung	lung
44	chr6:24774600-24776400	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr6:24774600-24776600	Active TSS	H1 Cell Line	embryonic stem cell
46	chr6:24774600-24776600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:24774600-24776600	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr6:24774600-24776600	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr6:24774600-24776600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr6:24774600-24776600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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