Variant report

Variant	rs10753409
Chromosome Location	chr1:225997475-225997476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr1:225997407-225998254	K562	blood:	n/a	n/a
2	POLR2A	chr1:225997413-225998142	U87	brain:	n/a	n/a
3	SP1	chr1:225997452-225998218	A549	lung:	n/a	n/a
4	MXI1	chr1:225997193-225998332	IMR90	lung:	n/a	n/a
5	POLR2A	chr1:225997445-225997978	HepG2	liver:	n/a	n/a
6	REST	chr1:225997330-225999216	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr1:225997379-225998099	PFSK-1	brain:	n/a	n/a
8	NRF1	chr1:225997265-225998282	SK-N-SH	brain:	n/a	chr1:225997781-225997792
9	POLR2A	chr1:225997437-225998198	Hela-S3	cervix:	n/a	n/a
10	NFIC	chr1:225997475-225998039	ECC-1	luminal epithelium:	n/a	n/a
11	MYBL2	chr1:225997425-225997943	HepG2	liver:	n/a	n/a
12	TAF1	chr1:225997459-225998056	H1-hESC	embryonic stem cell:	n/a	n/a
13	TCF7L2	chr1:225997350-225997914	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:225997421-225998330	K562	blood:	n/a	n/a
15	POLR2A	chr1:225997430-225998297	HepG2	liver:	n/a	n/a
16	POLR2A	chr1:225997393-225998323	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr1:225997442-225998367	SK-N-MC	brain:	n/a	n/a
18	TAF1	chr1:225997450-225997992	PFSK-1	brain:	n/a	n/a
19	MXI1	chr1:225997125-225998389	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr1:225997449-225998287	HUVEC	blood vessel:	n/a	n/a
21	MYBL2	chr1:225997413-225997839	HepG2	liver:	n/a	n/a
22	TCF7L2	chr1:225997377-225998173	HCT-116	colon:	n/a	n/a
23	POLR2A	chr1:225997470-225998118	K562	blood:	n/a	n/a
24	HEY1	chr1:225997431-225998090	HepG2	liver:	n/a	chr1:225997835-225997850
25	REST	chr1:225997428-225997916	A549	lung:	n/a	n/a
26	POLR2A	chr1:225997385-225998121	U87	brain:	n/a	n/a
27	HA-E2F1	chr1:225997222-225998288	MCF-7	breast:	n/a	chr1:225997843-225997853 chr1:225997840-225997850
28	POLR2A	chr1:225997471-225998226	MCF-7	breast:	n/a	n/a
29	POLR2A	chr1:225997392-225999160	H1-hESC	embryonic stem cell:	n/a	n/a
30	NR2F2	chr1:225997440-225997868	K562	blood:	n/a	n/a
31	POLR2A	chr1:225997471-225998260	MCF-7	breast:	n/a	n/a
32	POLR2A	chr1:225997198-225998441	HepG2	liver:	n/a	n/a
33	POLR2A	chr1:225997458-225998058	HCT-116	colon:	n/a	n/a
34	POLR2A	chr1:225997428-225998299	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr1:225997367-225998285	PFSK-1	brain:	n/a	n/a
36	POLR2A	chr1:225997306-225998167	HUVEC	blood vessel:	n/a	n/a
37	UBTF	chr1:225997282-225998308	K562	blood:	n/a	n/a
38	MAX	chr1:225997380-225998373	A549	lung:	n/a	n/a
39	ZNF263	chr1:225997302-225998286	HEK293-T-REx	kidney:	n/a	n/a
40	POLR2A	chr1:225997457-225998220	SK-N-SH	brain:	n/a	n/a
41	MAZ	chr1:225997430-225998350	IMR90	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:225962862..225967352-chr1:225996084..226002774,11	MCF-7	breast:
2	chr1:225989164..225991391-chr1:225995297..225997953,3	K562	blood:
3	chr1:225962294..225967531-chr1:225994011..226002080,11	K562	blood:
4	chr1:225997407..225998221-chr13:111367411..111367928,2	Hela-S3	cervix:
5	chr1:225963904..225970275-chr1:225994893..226001084,15	K562	blood:
6	chr1:225963814..225970754-chr1:225996230..226002908,14	MCF-7	breast:
7	chr1:225995407..225997753-chr1:226172864..226175325,2	K562	blood:

No data

Variant related genes	Relation type
EPHX1	TF binding region
ENSG00000234112	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10737418	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10737419	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737420	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799323	0.86[EUR][1000 genomes]
rs10799324	0.82[ASN][1000 genomes]
rs10915877	0.91[EUR][1000 genomes]
rs10915878	1.00[ASN][1000 genomes]
rs11583520	0.80[EUR][1000 genomes]
rs11808973	0.90[EUR][1000 genomes]
rs12727007	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12741681	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12744609	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12757220	0.85[EUR][1000 genomes]
rs1467143	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4559463	0.98[ASN][1000 genomes]
rs4653436	1.00[ASN][1000 genomes]
rs4653679	0.83[EUR][1000 genomes]
rs4653684	0.90[EUR][1000 genomes]
rs4653685	0.90[EUR][1000 genomes]
rs4653686	0.90[EUR][1000 genomes]
rs4653688	0.99[ASN][1000 genomes]
rs55736073	1.00[ASN][1000 genomes]
rs55954107	0.93[ASN][1000 genomes]
rs56195257	0.93[ASN][1000 genomes]
rs57440270	1.00[ASN][1000 genomes]
rs58241471	1.00[ASN][1000 genomes]
rs6426089	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6687036	0.91[EUR][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	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv945327	chr1:225991086-225998770	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225979600-225997800	Weak transcription	Gastric	stomach
2	chr1:225979800-225997600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:225979800-225997600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:225980000-225997600	Weak transcription	Left Ventricle	heart
5	chr1:225986000-225998000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:225991200-225997600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:225997000-225997600	Flanking Active TSS	HepG2	liver
8	chr1:225997200-225997600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:225997200-225997600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:225997200-225997600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:225997200-225997600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:225997200-225997600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:225997200-225997600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr1:225997200-225997600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:225997200-225997600	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr1:225997200-225997600	Enhancers	Colon Smooth Muscle	Colon
17	chr1:225997200-225997600	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr1:225997200-225997600	Enhancers	Pancreas	Pancrea
19	chr1:225997200-225997600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr1:225997200-225997600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr1:225997200-225997600	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr1:225997200-225997600	Enhancers	Thymus	Thymus
23	chr1:225997200-225997600	Flanking Active TSS	K562	blood
24	chr1:225997200-225998000	Active TSS	HMEC	breast
25	chr1:225997200-225998400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:225997200-225998400	Active TSS	HSMMtube	muscle
27	chr1:225997200-225998600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:225997200-225998600	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr1:225997200-225998600	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr1:225997200-225998600	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr1:225997200-225998600	Active TSS	Hela-S3	cervix
32	chr1:225997200-225998600	Active TSS	HSMM	muscle
33	chr1:225997200-225998800	Active TSS	Osteobl	bone
34	chr1:225997200-225999000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:225997200-225999000	Active TSS	Brain Hippocampus Middle	brain
36	chr1:225997200-225999200	Active TSS	Brain Angular Gyrus	brain
37	chr1:225997200-225999200	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr1:225997200-225999200	Active TSS	Rectal Smooth Muscle	rectum
39	chr1:225997200-225999600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:225997400-225997600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:225997400-225997600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr1:225997400-225997600	Active TSS	Primary B cells from cord blood	blood
43	chr1:225997400-225997600	Enhancers	Primary hematopoietic stem cells	blood
44	chr1:225997400-225997600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr1:225997400-225997600	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr1:225997400-225997600	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr1:225997400-225997600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:225997400-225997600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:225997400-225997600	Flanking Active TSS	Liver	Liver
50	chr1:225997400-225997600	Flanking Active TSS	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links