Variant report

Variant	rs58782668
Chromosome Location	chr10:5855743-5855744
allele	A/C
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	BHLHE40	chr10:5855115-5856469	HepG2	liver:	n/a	chr10:5856331-5856340 chr10:5855115-5855131 chr10:5855131-5855147 chr10:5856325-5856346 chr10:5855450-5855466 chr10:5856331-5856340
2	MYC	chr10:5854261-5856683	K562	blood:	n/a	chr10:5855795-5855804 chr10:5855794-5855805 chr10:5855797-5855806 chr10:5855793-5855806 chr10:5855795-5855804 chr10:5855794-5855805 chr10:5855794-5855804 chr10:5856330-5856341 chr10:5855795-5855805 chr10:5855903-5855922 chr10:5855795-5855804 chr10:5855786-5855802
3	USF2	chr10:5855291-5856416	GM12878	blood:	n/a	chr10:5856331-5856340 chr10:5856325-5856346 chr10:5855450-5855466 chr10:5856331-5856340
4	EP300	chr10:5855209-5856233	GM12878	blood:	n/a	chr10:5855318-5855332 chr10:5855822-5855838
5	POLR2A	chr10:5854493-5856423	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr10:5854538-5856364	Hela-S3	cervix:	n/a	n/a
7	GATA3	chr10:5854562-5856150	A549	lung:	n/a	n/a
8	PML	chr10:5854819-5856045	MCF-7	breast:	n/a	n/a
9	SPI1	chr10:5855140-5855759	GM12891	blood:	n/a	chr10:5855316-5855329
10	POLR2A	chr10:5854584-5856625	Hela-S3	cervix:	n/a	n/a
11	REST	chr10:5855612-5855887	K562	blood:	n/a	n/a
12	POLR2A	chr10:5854614-5857010	GM19193	blood:	n/a	n/a
13	POLR2A	chr10:5854681-5856051	Gliobla	brain:	n/a	n/a
14	PML	chr10:5854411-5856583	GM12878	blood:	n/a	n/a
15	YY1	chr10:5854807-5855923	SK-N-SH_RA	brain:	n/a	chr10:5855583-5855603 chr10:5855476-5855490 chr10:5855586-5855608 chr10:5855589-5855597 chr10:5855452-5855466 chr10:5855813-5855827 chr10:5854964-5854975 chr10:5855586-5855596 chr10:5855131-5855145 chr10:5855225-5855236
16	MAFK	chr10:5855001-5856813	GM12878	blood:	n/a	chr10:5856342-5856362 chr10:5856344-5856360 chr10:5856345-5856359 chr10:5856346-5856356 chr10:5856347-5856362
17	POLR2A	chr10:5855163-5855829	SK-N-MC	brain:	n/a	n/a
18	UBTF	chr10:5854563-5856395	K562	blood:	n/a	n/a
19	MXI1	chr10:5852991-5857043	SK-N-SH	brain:	n/a	chr10:5855794-5855803 chr10:5855794-5855803 chr10:5855796-5855805
20	GABPA	chr10:5855269-5855846	A549	lung:	n/a	chr10:5855676-5855685 chr10:5855648-5855657 chr10:5855813-5855822
21	RAD21	chr10:5854517-5856063	IMR90	lung:	n/a	chr10:5855466-5855480 chr10:5854594-5854604
22	ELK1	chr10:5854925-5856015	Hela-S3	cervix:	n/a	n/a
23	ETS1	chr10:5855117-5855802	A549	lung:	n/a	chr10:5855561-5855570 chr10:5855598-5855607 chr10:5855599-5855608 chr10:5855597-5855606 chr10:5855594-5855609 chr10:5855674-5855685 chr10:5855597-5855606 chr10:5855596-5855609
24	RUNX3	chr10:5854369-5856481	GM12878	blood:	n/a	n/a
25	POLR2A	chr10:5854682-5855976	A549	lung:	n/a	n/a
26	MYC	chr10:5854897-5856749	MCF10A-Er-Src	breast:	n/a	chr10:5855795-5855804 chr10:5855794-5855805 chr10:5855797-5855806 chr10:5855793-5855806 chr10:5855795-5855804 chr10:5855794-5855805 chr10:5855794-5855804 chr10:5856330-5856341 chr10:5855795-5855805 chr10:5855903-5855922 chr10:5855795-5855804 chr10:5855786-5855802
27	CHD2	chr10:5854643-5856057	Hela-S3	cervix:	n/a	chr10:5854926-5854936 chr10:5854992-5855002 chr10:5855258-5855265 chr10:5855561-5855570
28	TCF12	chr10:5855410-5855951	HepG2	liver:	n/a	n/a
29	GABPA	chr10:5855303-5855813	HepG2	liver:	n/a	chr10:5855676-5855685 chr10:5855648-5855657
30	POLR2A	chr10:5855517-5855973	HepG2	liver:	n/a	n/a
31	YY1	chr10:5855127-5855922	H1-hESC	embryonic stem cell:	n/a	chr10:5855583-5855603 chr10:5855476-5855490 chr10:5855586-5855608 chr10:5855589-5855597 chr10:5855452-5855466 chr10:5855813-5855827 chr10:5855586-5855596 chr10:5855131-5855145 chr10:5855225-5855236
32	POU2F2	chr10:5855119-5855888	GM12891	blood:	n/a	chr10:5855452-5855464 chr10:5855133-5855145
33	MXI1	chr10:5854198-5856428	GM12878	blood:	n/a	chr10:5855794-5855803 chr10:5855794-5855803 chr10:5855796-5855805
34	MXI1	chr10:5854735-5856459	HepG2	liver:	n/a	chr10:5855794-5855803 chr10:5855794-5855803 chr10:5855796-5855805
35	POLR2A	chr10:5854340-5856939	GM18526	blood:	n/a	n/a
36	TAF1	chr10:5854704-5855999	A549	lung:	n/a	n/a
37	CREB1	chr10:5855064-5855975	GM12878	blood:	n/a	n/a
38	SP4	chr10:5855120-5855771	H1-hESC	embryonic stem cell:	n/a	chr10:5855454-5855470 chr10:5855456-5855467 chr10:5855572-5855588
39	REST	chr10:5855433-5855991	ECC-1	luminal epithelium:	n/a	n/a
40	GTF2F1	chr10:5855221-5855833	K562	blood:	n/a	n/a
41	POLR2A	chr10:5855489-5855992	H1-hESC	embryonic stem cell:	n/a	n/a
42	MTA3	chr10:5854399-5856725	GM12878	blood:	n/a	n/a
43	MAX	chr10:5854549-5856500	HepG2	liver:	n/a	chr10:5855795-5855804 chr10:5855794-5855805 chr10:5855797-5855806 chr10:5855793-5855806 chr10:5855795-5855804 chr10:5855794-5855805 chr10:5855794-5855804 chr10:5856330-5856341 chr10:5855795-5855805 chr10:5855903-5855922 chr10:5855795-5855804 chr10:5855786-5855802
44	BRCA1	chr10:5855346-5856458	H1-hESC	embryonic stem cell:	n/a	chr10:5855561-5855570
45	RCOR1	chr10:5854856-5856654	GM12878	blood:	n/a	n/a
46	USF1	chr10:5855382-5855999	SK-N-SH_RA	brain:	n/a	chr10:5855450-5855466 chr10:5855793-5855804
47	USF1	chr10:5855577-5855962	GM12878	blood:	n/a	chr10:5855793-5855804
48	SIN3AK20	chr10:5855102-5856051	K562	blood:	n/a	n/a
49	POLR2A	chr10:5854345-5856432	HUVEC	blood vessel:	n/a	n/a
50	YY1	chr10:5854640-5856155	GM12892	blood:	n/a	chr10:5855583-5855603 chr10:5855476-5855490 chr10:5855586-5855608 chr10:5854737-5854748 chr10:5855589-5855597 chr10:5855452-5855466 chr10:5855813-5855827 chr10:5854964-5854975 chr10:5854788-5854797 chr10:5855586-5855596 chr10:5855131-5855145 chr10:5855225-5855236

No.	Distal block	Cell Line	Cell type
1	chr10:5725503..5729426-chr10:5853777..5860412,5	MCF-7	breast:
2	chr10:5853439..5857708-chr10:5926443..5936823,24	K562	blood:
3	chr10:5672014..5674575-chr10:5854060..5856479,2	MCF-7	breast:
4	chr10:5852473..5857853-chr10:5880942..5888645,8	MCF-7	breast:
5	chr10:5855140..5855745-chr6:26157980..26158656,2	Hela-S3	cervix:
6	chr10:5816487..5819223-chr10:5854186..5856565,2	MCF-7	breast:
7	chr10:5853517..5856397-chr10:6017987..6020051,2	MCF-7	breast:
8	chr10:5853575..5857221-chr10:5900529..5905112,5	MCF-7	breast:
9	chr10:5732056..5734929-chr10:5855542..5857938,2	K562	blood:
10	chr10:5487976..5490601-chr10:5853120..5856110,3	MCF-7	breast:
11	chr10:5664947..5667027-chr10:5854331..5857046,2	MCF-7	breast:
12	chr10:5854666..5855862-chr15:65588031..65589114,3	Hela-S3	cervix:
13	chr10:5851570..5858995-chr10:5881654..5887342,9	K562	blood:
14	chr10:5805727..5811403-chr10:5852267..5856532,7	MCF-7	breast:
15	chr10:5707157..5710880-chr10:5853405..5856185,3	K562	blood:
16	chr10:5855633..5857899-chr8:144821553..144823070,2	MCF-7	breast:
17	chr10:5815026..5819070-chr10:5852954..5857275,5	MCF-7	breast:
18	chr10:5708441..5709982-chr10:5853880..5856185,2	K562	blood:
19	chr10:5850869..5856128-chr10:5879241..5885807,8	K562	blood:
20	chr10:5725239..5729489-chr10:5854026..5858186,8	K562	blood:
21	chr10:5725427..5729550-chr10:5853446..5856157,4	MCF-7	breast:
22	chr10:5855209..5855820-chr19:45004202..45004956,2	Hela-S3	cervix:
23	chr10:5855392..5856073-chr16:57480920..57481571,2	HCT-116	colon:
24	chr10:5852595..5861125-chr10:5921136..5936216,31	MCF-7	breast:
25	chr10:5853820..5856785-chr10:5927225..5934067,15	K562	blood:
26	chr10:5853839..5856214-chr10:5942585..5945312,2	K562	blood:
27	chr10:5809711..5811648-chr10:5855446..5857250,2	K562	blood:
28	chr10:5852308..5856409-chr10:5935538..5939554,4	K562	blood:
29	chr10:5810148..5812616-chr10:5855203..5857512,4	K562	blood:
30	chr10:5853532..5857435-chr10:5928623..5934190,13	MCF-7	breast:
31	chr10:5855167..5855879-chr8:142011503..142012346,2	HCT-116	colon:

Variant related genes	Relation type
GDI2	TF binding region
ENSG00000272764	TF binding region
ENSG00000196372	Chromatin interaction
ENSG00000240180	Chromatin interaction
ENSG00000108021	Chromatin interaction
ENSG00000173848	Chromatin interaction
ENSG00000228685	Chromatin interaction
ENSG00000169398	Chromatin interaction
ENSG00000167384	Chromatin interaction
ENSG00000203499	Chromatin interaction
ENSG00000134470	Chromatin interaction
ENSG00000240577	Chromatin interaction
ENSG00000088682	Chromatin interaction
ENSG00000134461	Chromatin interaction
ENSG00000057608	Chromatin interaction
ENSG00000005194	Chromatin interaction
ENSG00000134452	Chromatin interaction
ENSG00000270427	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000158373	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11592184	1.00[ASN][1000 genomes]
rs11592260	1.00[ASN][1000 genomes]
rs11592964	1.00[ASN][1000 genomes]
rs11593253	0.88[ASN][1000 genomes]
rs11593616	0.83[ASN][1000 genomes]
rs11594153	1.00[ASN][1000 genomes]
rs11595445	1.00[ASN][1000 genomes]
rs11595457	1.00[ASN][1000 genomes]
rs11595970	0.88[ASN][1000 genomes]
rs11596815	0.83[ASN][1000 genomes]
rs11597597	0.88[ASN][1000 genomes]
rs11597948	1.00[ASN][1000 genomes]
rs11598319	1.00[ASN][1000 genomes]
rs2892072	0.83[ASN][1000 genomes]
rs4749325	0.80[ASN][1000 genomes]
rs57034347	1.00[ASN][1000 genomes]
rs57075354	1.00[ASN][1000 genomes]
rs59511159	0.83[ASN][1000 genomes]
rs60255716	0.83[ASN][1000 genomes]
rs61658636	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv515935	chr10:5820394-5869839	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS 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	28 gene(s)	inside rSNPs	diseases
6	nsv549896	chr10:5820394-5880066	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 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	chr10:5851600-5856200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr10:5851800-5856000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr10:5852000-5855800	Active TSS	HMEC	breast
4	chr10:5852000-5856800	Active TSS	NHLF	lung
5	chr10:5852400-5856600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr10:5852600-5856200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr10:5852600-5856400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr10:5852600-5856800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr10:5852800-5856400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr10:5852800-5856800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:5853000-5856000	Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr10:5853000-5856000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr10:5853000-5856000	Active TSS	Fetal Intestine Large	intestine
14	chr10:5853000-5856000	Active TSS	GM12878-XiMat	blood
15	chr10:5853000-5856000	Active TSS	NH-A	brain
16	chr10:5853000-5856200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:5853000-5856200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:5853000-5856200	Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr10:5853000-5856200	Active TSS	Brain Germinal Matrix	brain
20	chr10:5853000-5856200	Active TSS	A549	lung
21	chr10:5853000-5856200	Active TSS	NHDF-Ad	bronchial
22	chr10:5853000-5856600	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr10:5853000-5857000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr10:5853200-5856000	Active TSS	Muscle Satellite Cultured Cells	--
25	chr10:5853200-5856000	Active TSS	Brain Angular Gyrus	brain
26	chr10:5853200-5856000	Active TSS	Fetal Thymus	thymus
27	chr10:5853200-5856000	Active TSS	Hela-S3	cervix
28	chr10:5853200-5856200	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr10:5853200-5856200	Active TSS	HSMMtube	muscle
30	chr10:5853200-5856400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr10:5853200-5856400	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr10:5853200-5856400	Active TSS	Aorta	Aorta
33	chr10:5853200-5856400	Active TSS	Psoas Muscle	Psoas
34	chr10:5853200-5856400	Active TSS	Right Ventricle	heart
35	chr10:5853200-5856600	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr10:5853200-5856600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr10:5853200-5857000	Active TSS	H9 Cell Line	embryonic stem cell
38	chr10:5853400-5856200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr10:5853400-5856200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr10:5853400-5856400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr10:5853400-5856400	Active TSS	Ovary	ovary
42	chr10:5853400-5856600	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr10:5853400-5856600	Active TSS	Fetal Muscle Trunk	muscle
44	chr10:5853600-5856000	Active TSS	Duodenum Mucosa	Duodenum
45	chr10:5853600-5856000	Active TSS	Fetal Intestine Small	intestine
46	chr10:5853600-5856000	Active TSS	Fetal Kidney	kidney
47	chr10:5853600-5856000	Active TSS	Placenta	Placenta
48	chr10:5853600-5856000	Active TSS	NHEK	skin
49	chr10:5853600-5856200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr10:5853600-5856200	Active TSS	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links