Variant report

Variant	rs2893973
Chromosome Location	chr6:28697086-28697087
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:198)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:198 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF3	chr6:28696350-28697445	HCT-116	colon:	n/a	n/a
2	YY1	chr6:28697014-28697222	K562	blood:	n/a	n/a
3	MYC	chr6:28696585-28697336	NB4	blood:	n/a	n/a
4	ZBTB7A	chr6:28697002-28697222	K562	blood:	n/a	n/a
5	ETS1	chr6:28696854-28697341	K562	blood:	n/a	n/a
6	USF1	chr6:28696937-28697184	HepG2	liver:	n/a	n/a
7	MAX	chr6:28696905-28697403	A549	lung:	n/a	n/a
8	MXI1	chr6:28696962-28697262	HepG2	liver:	n/a	n/a
9	CREB1	chr6:28697002-28697214	A549	lung:	n/a	n/a
10	MYC	chr6:28697032-28697154	HUVEC	blood vessel:	n/a	n/a
11	ATF3	chr6:28696662-28697526	HCT-116	colon:	n/a	n/a
12	CTCF	chr6:28696960-28697110	GM12801	blood:	n/a	n/a
13	POLR2A	chr6:28697014-28697190	K562	blood:	n/a	n/a
14	NFIC	chr6:28696917-28697354	HepG2	liver:	n/a	n/a
15	MXI1	chr6:28696999-28697286	H1-hESC	embryonic stem cell:	n/a	n/a
16	PAX5	chr6:28696918-28697262	GM12878	blood:	n/a	n/a
17	CUX1	chr6:28696926-28697308	K562	blood:	n/a	n/a
18	ATF2	chr6:28696875-28697361	GM12878	blood:	n/a	n/a
19	MYC	chr6:28696916-28697284	Hela-S3	cervix:	n/a	n/a
20	MAX	chr6:28696617-28697314	NB4	blood:	n/a	n/a
21	GATA1	chr6:28696783-28697195	PBDEFetal	blood:	n/a	n/a
22	MAX	chr6:28696807-28697452	A549	lung:	n/a	n/a
23	ZNF143	chr6:28696760-28697318	K562	blood:	n/a	n/a
24	ELF1	chr6:28696931-28697356	HepG2	liver:	n/a	n/a
25	USF1	chr6:28696996-28697152	SK-N-SH_RA	brain:	n/a	n/a
26	BCLAF1	chr6:28696658-28697427	GM12878	blood:	n/a	chr6:28697022-28697031
27	TEAD4	chr6:28696907-28697303	MCF-7	breast:	n/a	n/a
28	MAZ	chr6:28696940-28697327	K562	blood:	n/a	n/a
29	STAT5A	chr6:28696949-28697302	GM12878	blood:	n/a	chr6:28697022-28697033
30	ATF2	chr6:28696844-28697291	GM12878	blood:	n/a	n/a
31	E2F6	chr6:28697042-28697209	K562	blood:	n/a	n/a
32	ZMIZ1	chr6:28696650-28697606	K562	blood:	n/a	n/a
33	TBP	chr6:28696721-28697315	K562	blood:	n/a	n/a
34	MYC	chr6:28696911-28697527	MCF10A-Er-Src	breast:	n/a	n/a
35	MAX	chr6:28696513-28697351	Hela-S3	cervix:	n/a	n/a
36	TCF12	chr6:28697017-28697213	H1-hESC	embryonic stem cell:	n/a	n/a
37	ETS1	chr6:28696969-28697331	A549	lung:	n/a	n/a
38	BHLHE40	chr6:28696702-28697302	K562	blood:	n/a	n/a
39	MYC	chr6:28697031-28697166	Hela-S3	cervix:	n/a	n/a
40	MYC	chr6:28696633-28697382	K562	blood:	n/a	n/a
41	TEAD4	chr6:28696774-28697441	A549	lung:	n/a	n/a
42	TBL1XR1	chr6:28696540-28697353	K562	blood:	n/a	n/a
43	YY1	chr6:28696970-28697285	GM12878	blood:	n/a	n/a
44	IRF1	chr6:28696939-28697313	K562	blood:	n/a	chr6:28697021-28697035 chr6:28697016-28697037 chr6:28697019-28697033 chr6:28697021-28697038 chr6:28697022-28697036 chr6:28697020-28697034 chr6:28697018-28697032 chr6:28697020-28697033 chr6:28697020-28697033 chr6:28697022-28697032 chr6:28697023-28697034 chr6:28697020-28697033 chr6:28697022-28697033
45	CHD1	chr6:28696480-28697693	IMR90	lung:	n/a	n/a
46	MAX	chr6:28696432-28697457	HCT-116	colon:	n/a	n/a
47	ARID3A	chr6:28696570-28697387	K562	blood:	n/a	n/a
48	MAX	chr6:28696874-28697312	SK-N-SH	brain:	n/a	n/a
49	ETS1	chr6:28696863-28697380	GM12878	blood:	n/a	n/a
50	THAP1	chr6:28697003-28697234	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28695857..28698165-chr6:28761272..28763967,2	K562	blood:
2	chr6:28695149..28697621-chr6:28743260..28745137,3	K562	blood:
3	chr6:28694465..28699409-chr6:28701823..28706376,12	K562	blood:
4	chr6:28695047..28697144-chr6:28756622..28759292,2	K562	blood:
5	chr6:28666298..28671313-chr6:28695437..28699521,5	K562	blood:
6	chr6:28694799..28697435-chr6:28950609..28952532,2	K562	blood:
7	chr6:28695842..28698712-chr6:28863478..28865661,2	K562	blood:
8	chr6:28695559..28699343-chr6:28721391..28727067,6	K562	blood:
9	chr6:28695145..28698066-chr6:28723238..28727067,5	K562	blood:
10	chr6:28695685..28697357-chr6:28761253..28763967,2	K562	blood:

No data

Variant related genes	Relation type
RPSAP2	TF binding region
ENSG00000221191	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000265764	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12660605	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1539584	0.89[ASN][1000 genomes]
rs2394130	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2893970	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3869043	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56404349	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72844382	0.89[ASN][1000 genomes]
rs9257110	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9257111	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9257112	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9257114	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257115	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9257117	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9257124	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9257128	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9257129	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9257131	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9257132	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9257148	0.82[ASN][1000 genomes]
rs9257149	0.82[ASN][1000 genomes]
rs9257150	0.82[ASN][1000 genomes]
rs9257157	0.81[ASN][1000 genomes]
rs9257175	0.81[ASN][1000 genomes]
rs9348812	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9368571	0.88[ASN][1000 genomes]
rs9380085	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9380086	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9393928	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28694200-28697800	Active TSS	K562	blood
2	chr6:28695800-28698000	Active TSS	NH-A	brain
3	chr6:28695800-28698200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:28695800-28698200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:28696000-28697200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:28696000-28697400	Active TSS	Muscle Satellite Cultured Cells	--
7	chr6:28696000-28697400	Active TSS	Hela-S3	cervix
8	chr6:28696000-28697600	Active TSS	HSMMtube	muscle
9	chr6:28696000-28697600	Active TSS	NHEK	skin
10	chr6:28696000-28697600	Active TSS	Osteobl	bone
11	chr6:28696000-28697800	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr6:28696000-28698000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:28696000-28698000	Active TSS	HMEC	breast
14	chr6:28696200-28697200	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr6:28696200-28697200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:28696200-28697200	Active TSS	HUVEC	blood vessel
17	chr6:28696200-28697400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
18	chr6:28696200-28697400	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
19	chr6:28696200-28697600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:28696200-28697600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:28696200-28697600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr6:28696200-28697600	Bivalent/Poised TSS	HepG2	liver
23	chr6:28696200-28697800	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr6:28696200-28697800	Active TSS	H1 Cell Line	embryonic stem cell
25	chr6:28696200-28697800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:28696200-28697800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:28696200-28698000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:28696200-28698000	Active TSS	Ovary	ovary
29	chr6:28696200-28698400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
30	chr6:28696200-28698400	Active TSS	A549	lung
31	chr6:28696400-28697200	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
32	chr6:28696400-28697200	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:28696400-28697200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:28696400-28697200	Active TSS	Aorta	Aorta
35	chr6:28696400-28697200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:28696400-28697200	Active TSS	Colonic Mucosa	Colon
37	chr6:28696400-28697200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
38	chr6:28696400-28697200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
39	chr6:28696400-28697200	Active TSS	Placenta	Placenta
40	chr6:28696400-28697200	Active TSS	Gastric	stomach
41	chr6:28696400-28697200	Bivalent/Poised TSS	Left Ventricle	heart
42	chr6:28696400-28697200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
43	chr6:28696400-28697200	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr6:28696400-28697200	Active TSS	Rectal Smooth Muscle	rectum
45	chr6:28696400-28697200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
46	chr6:28696400-28697200	Active TSS	NHLF	lung
47	chr6:28696400-28697400	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr6:28696400-28697400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
49	chr6:28696400-28697400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr6:28696400-28697400	Bivalent/Poised TSS	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links