Variant report

Variant	rs1528878
Chromosome Location	chr10:54073577-54073578
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:108)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:108 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr10:54073306-54074631	HepG2	liver:	n/a	n/a
2	MAX	chr10:54073032-54075312	A549	lung:	n/a	n/a
3	POLR2A	chr10:54072994-54075187	MCF-7	breast:	n/a	n/a
4	RXRA	chr10:54073541-54074702	SK-N-SH	brain:	n/a	chr10:54074160-54074169
5	RFX5	chr10:54073484-54074380	HepG2	liver:	n/a	n/a
6	MAZ	chr10:54073295-54075277	IMR90	lung:	n/a	n/a
7	MAFK	chr10:54073545-54073892	HepG2	liver:	n/a	n/a
8	REST	chr10:54072922-54075349	A549	lung:	n/a	chr10:54073933-54073946
9	CEBPB	chr10:54073328-54074677	A549	lung:	n/a	n/a
10	POLR2A	chr10:54072977-54075692	Gliobla	brain:	n/a	n/a
11	MAFK	chr10:54073465-54073816	HepG2	liver:	n/a	n/a
12	SP1	chr10:54073169-54075305	A549	lung:	n/a	chr10:54074927-54074937 chr10:54074910-54074919 chr10:54074913-54074927 chr10:54074927-54074936 chr10:54074926-54074938 chr10:54074905-54074914 chr10:54074909-54074921 chr10:54074923-54074937 chr10:54074911-54074920 chr10:54074926-54074938 chr10:54074910-54074920 chr10:54074909-54074921
13	ARID3A	chr10:54072857-54074523	HepG2	liver:	n/a	n/a
14	REST	chr10:54073522-54074886	A549	lung:	n/a	chr10:54073933-54073946
15	RFX5	chr10:54073572-54074820	Hela-S3	cervix:	n/a	n/a
16	GATA3	chr10:54072994-54074515	MCF-7	breast:	n/a	n/a
17	CEBPD	chr10:54073575-54074411	HepG2	liver:	n/a	n/a
18	POLR2A	chr10:54073464-54075557	HUVEC	blood vessel:	n/a	n/a
19	MAFK	chr10:54073480-54073799	IMR90	lung:	n/a	n/a
20	EP300	chr10:54073486-54074630	HepG2	liver:	n/a	chr10:54074160-54074174
21	NR2F2	chr10:54073540-54074356	MCF-7	breast:	n/a	n/a
22	GATA2	chr10:54072878-54074785	SH-SY5Y	brain:	n/a	n/a
23	CHD2	chr10:54073312-54074500	H1-hESC	embryonic stem cell:	n/a	n/a
24	RAD21	chr10:54073545-54074613	Hela-S3	cervix:	n/a	chr10:54074080-54074090 chr10:54074078-54074091
25	TCF12	chr10:54073220-54074671	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr10:54073525-54079363	HUVEC	blood vessel:	n/a	n/a
27	MYBL2	chr10:54073553-54074694	HepG2	liver:	n/a	n/a
28	TCF12	chr10:54073250-54073773	H1-hESC	embryonic stem cell:	n/a	n/a
29	TCF12	chr10:54073393-54073619	H1-hESC	embryonic stem cell:	n/a	n/a
30	GATA2	chr10:54072971-54074768	HUVEC	blood vessel:	n/a	n/a
31	NR2F2	chr10:54073459-54074614	MCF-7	breast:	n/a	n/a
32	POLR2A	chr10:54073092-54080655	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr10:54073389-54074853	HEK293	kidney:	n/a	n/a
34	MYC	chr10:54073505-54074517	MCF10A-Er-Src	breast:	n/a	n/a
35	CTCF	chr10:54072615-54075091	A549	lung:	n/a	chr10:54073933-54073946
36	YY1	chr10:54073381-54073619	HCT-116	colon:	n/a	n/a
37	MAFK	chr10:54073418-54074534	Hela-S3	cervix:	n/a	chr10:54074098-54074108
38	GATA3	chr10:54073034-54075851	A549	lung:	n/a	chr10:54075334-54075351 chr10:54075069-54075076 chr10:54075068-54075078
39	MBD4	chr10:54073552-54074724	HepG2	liver:	n/a	n/a
40	TCF12	chr10:54073532-54074560	A549	lung:	n/a	n/a
41	POLR2A	chr10:54073497-54074563	HepG2	liver:	n/a	n/a
42	HEY1	chr10:54073574-54076765	HepG2	liver:	n/a	n/a
43	GATA3	chr10:54072834-54077297	SK-N-SH	brain:	n/a	chr10:54076036-54076046 chr10:54075334-54075351 chr10:54075069-54075076 chr10:54075068-54075078
44	BCL3	chr10:54072807-54075220	A549	lung:	n/a	chr10:54074906-54074919 chr10:54074911-54074920
45	POLR2A	chr10:54072864-54080901	ProgFib	skin:	n/a	n/a
46	FOXA2	chr10:54073400-54074645	A549	lung:	n/a	n/a
47	TCF7L2	chr10:54072515-54074594	HEK293	kidney:	n/a	chr10:54073942-54073956
48	MAX	chr10:54073427-54073700	H1-hESC	embryonic stem cell:	n/a	n/a
49	MAX	chr10:54072918-54075448	A549	lung:	n/a	chr10:54075399-54075409
50	BCL3	chr10:54073209-54074735	A549	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:54073548-54073598	A549	lung:	n/a
2	chr10:54073548-54073598	SK-N-MC	brain:	n/a
3	chr10:54073548-54073598	HEEpiC	esophagus:	n/a
4	chr10:54073548-54073598	HCT-116	colon:	n/a
5	chr10:54073548-54073598	HAEpiC	amniotic membrane:	n/a
6	chr10:54073548-54073598	HNPCEpiC	eye:	n/a
7	chr10:54073548-54073598	AG09319	gingival:	n/a
8	chr10:54073548-54073598	U87	brain:	n/a
9	chr10:54073548-54073598	K562	blood:	n/a
10	chr10:54073548-54073598	HCF	heart:	n/a
11	chr10:54073548-54073598	GM12891	blood:	n/a
12	chr10:54073548-54073598	SKMC	muscle:	n/a
13	chr10:54073548-54073598	NHBE	bronchial:	n/a
14	chr10:54073548-54073598	HPAEpiC	pulmonary alveolar:	n/a
15	chr10:54073548-54073598	Jurkat	blood:	n/a
16	chr10:54073548-54073598	HUVEC	blood vessel:	n/a
17	chr10:54073548-54073598	ECC-1	luminal epithelium:	n/a
18	chr10:54073548-54073598	AG09309	skin:	n/a
19	chr10:54073548-54073598	HIPEpiC	eye:	n/a
20	chr10:54073548-54073598	Caco-2	colon:	n/a
21	chr10:54073548-54073598	AG04450	lung:	fetal
22	chr10:54073548-54073598	RPTEC	kidney:	n/a
23	chr10:54073548-54073598	GM12878	blood:	n/a
24	chr10:54073548-54073598	ProgFib	skin:	n/a
25	chr10:54073548-54073598	MCF10A-Er-Src	breast:	n/a
26	chr10:54073548-54073598	HCM	heart:	n/a
27	chr10:54073548-54073598	NB4	blood:	n/a
28	chr10:54073548-54073598	HRPEpiC	eye:	n/a
29	chr10:54073548-54073598	PFSK-1	brain:	n/a
30	chr10:54073548-54073598	HEK293	kidney:	embryo
31	chr10:54073548-54073598	Hepatocyte	liver:	n/a
32	chr10:54073548-54073598	PrEC	prostate:	n/a
33	chr10:54073548-54073598	IMR90	lung:	fetal
34	chr10:54073548-54073598	AG10803	skin:	n/a
35	chr10:54073548-54073598	AG04449	skin:	fetal
36	chr10:54073548-54073598	Hela-S3	cervix:	n/a
37	chr10:54073548-54073598	SK-N-SH	brain:	n/a
38	chr10:54073548-54073598	HRCEpiC	kidney:	n/a
39	chr10:54073548-54073598	BE2_C	brain:	n/a
40	chr10:54073548-54073598	HMEC	breast:	n/a
41	chr10:54073548-54073598	BJ	skin:	n/a
42	chr10:54073548-54073598	SK-N-SH_RA	brain:	n/a
43	chr10:54073548-54073598	NHDF-neo	bronchial:	n/a
44	chr10:54073548-54073598	H1-hESC	embryonic stem cell:	embryo
45	chr10:54073548-54073598	PANC-1	pancreas:	n/a
46	chr10:54073548-54073598	NT2-D1	testis:	n/a
47	chr10:54073548-54073598	GM12892	blood:	n/a
48	chr10:54073548-54073598	MCF-7	breast:	n/a
49	chr10:54073548-54073598	NH-A	brain:	n/a
50	chr10:54073548-54073598	HCPEpiC	choroid plexus:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:54065577..54083492-chr10:54193846..54218961,120	MCF-7	breast:
2	chr10:54073525..54075924-chr10:54146848..54149629,2	MCF-7	breast:
3	chr10:54073396..54076476-chr10:54227833..54231095,3	MCF-7	breast:
4	chr10:54073032..54076598-chr10:54229475..54234592,10	MCF-7	breast:
5	chr10:54071324..54082180-chr10:54192987..54217560,81	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MBL2-5	chr10:54073394-54073888	ENSG00000236671
2	lnc-MBL2-5	chr10:54073394-54073870	NONHSAT013418
3	lnc-MBL2-5	chr10:54073394-54073888	NR_038277

No data

Variant related genes	Relation type
DKK1	TF binding region
DKK1	CpG island
ENSG00000231131	Chromatin interaction
ENSG00000213657	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1528879	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59544809	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs60133922	0.81[AFR][1000 genomes]
rs7069912	1.00[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	nsv1045692	chr10:53301450-54086823	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv532194	chr10:53746620-54735550	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv895399	chr10:53900872-54219820	Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv895400	chr10:54073294-54094359	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54068800-54073800	Weak transcription	Lung	lung
2	chr10:54072600-54073600	Flanking Active TSS	HMEC	breast
3	chr10:54072600-54075000	Active TSS	A549	lung
4	chr10:54072800-54073600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
5	chr10:54072800-54073600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:54072800-54073600	Flanking Bivalent TSS/Enh	HepG2	liver
7	chr10:54072800-54073600	Flanking Active TSS	HUVEC	blood vessel
8	chr10:54072800-54073600	Flanking Active TSS	NH-A	brain
9	chr10:54072800-54073800	Bivalent Enhancer	Liver	Liver
10	chr10:54072800-54073800	Flanking Active TSS	Brain Angular Gyrus	brain
11	chr10:54072800-54073800	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr10:54072800-54073800	Active TSS	Right Ventricle	heart
13	chr10:54072800-54073800	Flanking Active TSS	NHEK	skin
14	chr10:54072800-54074400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr10:54072800-54074400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr10:54072800-54074400	Active TSS	Right Atrium	heart
17	chr10:54072800-54074800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
18	chr10:54072800-54074800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
19	chr10:54072800-54075200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr10:54072800-54075200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:54072800-54075800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr10:54072800-54075800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr10:54073000-54073600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr10:54073000-54073600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr10:54073000-54073600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr10:54073000-54073600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr10:54073000-54073600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
28	chr10:54073000-54073600	Bivalent/Poised TSS	Fetal Brain Female	brain
29	chr10:54073000-54073600	Enhancers	Pancreas	Pancrea
30	chr10:54073000-54073600	Flanking Active TSS	NHLF	lung
31	chr10:54073000-54073800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
32	chr10:54073000-54073800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr10:54073000-54073800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
34	chr10:54073000-54073800	Enhancers	Gastric	stomach
35	chr10:54073000-54073800	Flanking Active TSS	Osteobl	bone
36	chr10:54073000-54074200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
37	chr10:54073000-54074200	Flanking Bivalent TSS/Enh	Placenta	Placenta
38	chr10:54073000-54074400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr10:54073000-54074800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
40	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr10:54073000-54074800	Bivalent/Poised TSS	Aorta	Aorta
42	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
43	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
44	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
45	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
46	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
47	chr10:54073000-54074800	Enhancers	Spleen	Spleen
48	chr10:54073000-54075000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
49	chr10:54073000-54075800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr10:54073200-54073600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links