Variant report

Variant	rs9898606
Chromosome Location	chr17:45972163-45972164
allele	A/G
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	POLR2A	chr17:45972099-45974517	GM12878	blood:	n/a	n/a
2	POLR2A	chr17:45972080-45974536	PBDE	blood:	n/a	n/a
3	RCOR1	chr17:45971977-45973573	K562	blood:	n/a	n/a
4	SP1	chr17:45972136-45974646	HCT-116	colon:	n/a	chr17:45973879-45973891 chr17:45973880-45973889 chr17:45973795-45973807 chr17:45973762-45973771 chr17:45973298-45973310 chr17:45973298-45973310 chr17:45973963-45973976 chr17:45973795-45973807 chr17:45973299-45973313 chr17:45973300-45973309 chr17:45973880-45973894 chr17:45973796-45973805 chr17:45973797-45973806 chr17:45973008-45973017 chr17:45973881-45973890 chr17:45973880-45973889 chr17:45973879-45973891 chr17:45973195-45973216 chr17:45973299-45973308 chr17:45973477-45973498 chr17:45973355-45973376
5	TAL1	chr17:45972049-45972523	K562	blood:	n/a	n/a
6	EGR1	chr17:45971777-45972163	K562	blood:	n/a	chr17:45971984-45972006
7	SIN3AK20	chr17:45971760-45975069	MCF-7	breast:	n/a	n/a
8	MAFF	chr17:45972050-45972495	K562	blood:	n/a	n/a
9	POLR2A	chr17:45971826-45975269	K562	blood:	n/a	n/a
10	ATF1	chr17:45971899-45972280	K562	blood:	n/a	n/a
11	MYC	chr17:45972028-45974397	K562	blood:	n/a	chr17:45973375-45973385 chr17:45973882-45973892 chr17:45973720-45973730 chr17:45973742-45973752
12	ZNF384	chr17:45972124-45972570	GM12878	blood:	n/a	n/a
13	RCOR1	chr17:45971800-45972163	K562	blood:	n/a	n/a
14	CTCF	chr17:45971791-45972334	K562	blood:	n/a	chr17:45971958-45971967 chr17:45971947-45971968 chr17:45971952-45971970
15	MAFK	chr17:45971978-45972756	K562	blood:	n/a	n/a
16	POLR2A	chr17:45972120-45974333	K562	blood:	n/a	n/a
17	POLR2A	chr17:45971993-45974835	MCF10A-Er-Src	breast:	n/a	n/a
18	GATA2	chr17:45971863-45972330	K562	blood:	n/a	n/a
19	EP300	chr17:45972113-45973483	A549	lung:	n/a	n/a
20	POLR2A	chr17:45971993-45972457	HepG2	liver:	n/a	n/a
21	JUND	chr17:45971862-45973992	K562	blood:	n/a	chr17:45973063-45973071 chr17:45973204-45973213
22	MTA3	chr17:45972070-45974627	GM12878	blood:	n/a	n/a
23	ZNF384	chr17:45971843-45973340	K562	blood:	n/a	n/a
24	BRCA1	chr17:45972141-45974272	Hela-S3	cervix:	n/a	n/a
25	EP300	chr17:45971836-45972538	K562	blood:	n/a	chr17:45971978-45971992

No.	Distal block	Cell Line	Cell type
1	chr17:45939167..45942098-chr17:45971547..45974421,3	MCF-7	breast:
2	chr17:45921031..45932631-chr17:45970978..45975136,16	K562	blood:
3	chr17:45961070..45963855-chr17:45969315..45972508,3	MCF-7	breast:
4	chr17:45918236..45922252-chr17:45971224..45975227,6	K562	blood:
5	chr17:45916146..45920179-chr17:45971137..45974158,6	K562	blood:
6	chr17:45928506..45931150-chr17:45970978..45973009,3	K562	blood:
7	chr17:45972027..45973023-chr7:104653166..104654152,2	Hela-S3	cervix:
8	chr17:45908246..45910427-chr17:45971152..45975040,4	K562	blood:
9	chr17:45971907..45976557-chr17:46046916..46050358,7	K562	blood:
10	chr17:45940066..45942242-chr17:45971529..45973445,2	K562	blood:
11	chr17:45970859..45972608-chr17:46032842..46035268,2	MCF-7	breast:
12	chr17:45970460..45972563-chr17:46022698..46024449,2	K562	blood:
13	chr17:45944883..45946724-chr17:45969960..45972616,2	MCF-7	breast:
14	chr17:45971266..45974117-chr17:46049059..46051074,2	MCF-7	breast:
15	chr17:45943296..45945014-chr17:45970935..45972953,2	K562	blood:
16	chr17:45906763..45908800-chr17:45971600..45974534,3	MCF-7	breast:
17	chr17:45895199..45899793-chr17:45971655..45976847,6	K562	blood:
18	chr17:45970912..45974701-chr17:46018890..46021752,3	K562	blood:
19	chr17:45931240..45934148-chr17:45971745..45974291,3	MCF-7	breast:
20	chr17:45892358..45894158-chr17:45971060..45972712,2	MCF-7	breast:
21	chr17:45915230..45925590-chr17:45966201..45976437,35	MCF-7	breast:
22	chr17:45969751..45975935-chr17:46032072..46038613,14	MCF-7	breast:
23	chr17:45907261..45910696-chr17:45969933..45974046,5	MCF-7	breast:
24	chr17:45971907..45974928-chr17:46046916..46050084,5	K562	blood:
25	chr17:45970281..45975378-chr17:46022719..46027732,11	MCF-7	breast:
26	chr17:45913484..45922782-chr17:45969196..45975741,24	MCF-7	breast:
27	chr17:45914946..45918155-chr17:45971112..45974378,4	K562	blood:
28	chr17:45971215..45974947-chr17:46046480..46050487,6	MCF-7	breast:
29	chr17:45971510..45977679-chr17:46016123..46021422,20	MCF-7	breast:
30	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
31	chr17:45923146..45930414-chr17:45970842..45976007,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SP6-2	chr17:45969220-45973158	ENSG00000264920.1

Variant related genes	Relation type
SP2	TF binding region
ENSG00000189120	Chromatin interaction
ENSG00000159111	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000141294	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000264019	Chromatin interaction
ENSG00000264243	Chromatin interaction
ENSG00000263798	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000006025	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000167183	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11650451	1.00[CHB][hapmap]
rs12449469	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12450706	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12452142	1.00[AMR][1000 genomes]
rs16947078	1.00[CHB][hapmap]
rs17700839	1.00[CHB][hapmap]
rs28547560	0.83[AFR][1000 genomes]
rs28585388	1.00[AMR][1000 genomes]
rs28607433	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28690817	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9892852	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9894825	0.83[AFR][1000 genomes]
rs9896981	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9897154	1.00[AMR][1000 genomes]
rs9898089	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9901308	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9902511	1.00[AMR][1000 genomes]
rs9903922	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9906184	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9908317	0.83[AFR][1000 genomes]
rs9909897	1.00[AMR][1000 genomes]
rs9910263	1.00[AMR][1000 genomes]
rs9916700	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS 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 target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45960000-45972200	Weak transcription	HUVEC	blood vessel
2	chr17:45963400-45972200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr17:45963400-45972600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:45963600-45972200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr17:45963600-45972400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:45967800-45972200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr17:45967800-45972400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr17:45967800-45972400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:45969600-45972200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr17:45970200-45972200	Weak transcription	Ovary	ovary
11	chr17:45970800-45972200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr17:45971200-45972200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr17:45971400-45972200	Enhancers	Primary hematopoietic stem cells	blood
14	chr17:45971400-45972200	Enhancers	HepG2	liver
15	chr17:45971400-45972400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr17:45971400-45974600	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr17:45971600-45972200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:45971600-45972200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr17:45971600-45972200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr17:45971600-45972200	Enhancers	Liver	Liver
21	chr17:45971600-45972200	Enhancers	Fetal Muscle Leg	muscle
22	chr17:45971600-45972400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr17:45971600-45972400	Enhancers	Brain Cingulate Gyrus	brain
24	chr17:45971600-45972600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr17:45971600-45972600	Weak transcription	Gastric	stomach
26	chr17:45971600-45972600	Enhancers	Spleen	Spleen
27	chr17:45971800-45972200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr17:45971800-45972200	Enhancers	Primary B cells from cord blood	blood
29	chr17:45971800-45972200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr17:45971800-45972200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr17:45971800-45972200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr17:45971800-45972200	Enhancers	Esophagus	oesophagus
33	chr17:45971800-45972200	Enhancers	Fetal Brain Male	brain
34	chr17:45971800-45972200	Enhancers	Fetal Intestine Large	intestine
35	chr17:45971800-45972200	Enhancers	Fetal Stomach	stomach
36	chr17:45971800-45972200	Weak transcription	Fetal Thymus	thymus
37	chr17:45971800-45972200	Flanking Active TSS	Stomach Mucosa	stomach
38	chr17:45971800-45972200	Enhancers	A549	lung
39	chr17:45971800-45972200	Enhancers	NHLF	lung
40	chr17:45971800-45972400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr17:45971800-45972400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr17:45971800-45972400	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr17:45971800-45972400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr17:45971800-45972400	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr17:45971800-45972400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr17:45971800-45972400	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr17:45971800-45972400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr17:45971800-45972400	Enhancers	Brain Germinal Matrix	brain
49	chr17:45971800-45972400	Enhancers	Fetal Intestine Small	intestine
50	chr17:45971800-45972400	Weak transcription	Left Ventricle	heart

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