Variant report

Variant	rs59956612
Chromosome Location	chr1:149855734-149855735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:34)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr1:149855208-149857964	MCF-7	breast:	n/a	n/a
2	CHD1	chr1:149854894-149860797	IMR90	lung:	n/a	n/a
3	POLR2A	chr1:149855068-149855984	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:149855250-149855874	H1-hESC	embryonic stem cell:	n/a	n/a
5	CHD2	chr1:149855227-149860558	K562	blood:	n/a	n/a
6	POLR2A	chr1:149855058-149855881	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr1:149855265-149860844	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:149855109-149860572	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:149855027-149855831	IMR90	lung:	n/a	n/a
10	POLR2A	chr1:149855079-149860735	PBDE	blood:	n/a	n/a
11	SIN3AK20	chr1:149854723-149856194	K562	blood:	n/a	n/a
12	MAFF	chr1:149855628-149857664	K562	blood:	n/a	n/a
13	GATA1	chr1:149855381-149860460	PBDE	blood:	n/a	chr1:149859655-149859665
14	POLR2A	chr1:149854930-149863498	H1-hESC	embryonic stem cell:	n/a	n/a
15	GATA3	chr1:149855456-149856096	SH-SY5Y	brain:	n/a	n/a
16	BCLAF1	chr1:149855613-149860868	K562	blood:	n/a	chr1:149859834-149859843
17	ZNF143	chr1:149855462-149855738	K562	blood:	n/a	n/a
18	BCLAF1	chr1:149854854-149860655	K562	blood:	n/a	chr1:149859834-149859843
19	RCOR1	chr1:149855457-149855768	K562	blood:	n/a	n/a
20	PML	chr1:149854976-149860749	K562	blood:	n/a	n/a
21	HEY1	chr1:149855072-149862207	K562	blood:	n/a	n/a
22	POLR2A	chr1:149853202-149861769	K562	blood:	n/a	n/a
23	POLR2A	chr1:149855597-149855748	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr1:149854904-149860374	K562	blood:	n/a	n/a
25	POLR2A	chr1:149852655-149863016	K562	blood:	n/a	n/a
26	POLR2A	chr1:149855158-149860905	H1-hESC	embryonic stem cell:	n/a	n/a
27	TAL1	chr1:149855518-149860965	K562	blood:	n/a	n/a
28	CEBPD	chr1:149854797-149857895	K562	blood:	n/a	n/a
29	POLR2A	chr1:149855067-149855934	K562	blood:	n/a	n/a

No data

(count:34 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:149813928..149823076-chr1:149854513..149862208,33	K562	blood:
2	chr1:149855129..149857498-chr5:89704322..89707412,3	MCF-7	breast:
3	chr1:149813687..149823244-chr1:149851297..149861525,76	MCF-7	breast:
4	chr1:149854948..149862391-chr1:150036900..150043965,32	MCF-7	breast:
5	chr1:149854988..149857617-chr17:41463714..41465373,2	MCF-7	breast:
6	chr1:149855608..149858042-chr2:122287133..122289817,2	MCF-7	breast:
7	chr1:149855028..149856935-chr19:27731051..27732710,2	MCF-7	breast:
8	chr1:149855502..149862139-chr17:57919672..57925878,9	MCF-7	breast:
9	chr1:149855162..149857708-chr1:149989718..149991505,2	K562	blood:
10	chr1:149853005..149861438-chr1:149978765..149991065,34	MCF-7	breast:
11	chr1:149854015..149856370-chr1:150208548..150210242,2	K562	blood:
12	chr1:145012976..145015960-chr1:149855558..149857553,2	K562	blood:
13	chr1:149855727..149858641-chr12:53341996..53343624,2	MCF-7	breast:
14	chr1:149854493..149857543-chr1:150205642..150209328,3	MCF-7	breast:
15	chr1:149854540..149863300-chr1:149979575..149985253,19	K562	blood:
16	chr1:149855702..149858196-chr17:57831980..57834656,2	MCF-7	breast:
17	chr1:149855536..149863300-chr1:149977462..149985642,29	K562	blood:
18	chr1:149853460..149855808-chr1:150158235..150161131,2	K562	blood:
19	chr1:149855076..149857631-chr17:58601286..58603694,2	MCF-7	breast:
20	chr1:149813697..149823354-chr1:149851773..149862006,115	MCF-7	breast:
21	chr1:149855155..149857898-chr3:184077901..184080591,2	MCF-7	breast:
22	chr1:149853918..149856291-chr1:150026219..150029011,2	K562	blood:
23	chr1:149855495..149858087-chr1:167906721..167908261,2	K562	blood:
24	chr1:149855140..149858335-chr17:56706223..56709369,3	MCF-7	breast:
25	chr1:149855640..149857208-chr4:83290847..83292971,2	K562	blood:
26	chr1:149813771..149823366-chr1:149853740..149862208,36	K562	blood:
27	chr1:149844868..149846409-chr1:149855462..149857720,2	K562	blood:
28	chr1:145003130..145005875-chr1:149855420..149857105,2	K562	blood:
29	chr1:149854324..149859746-chr20:45984655..45988969,6	MCF-7	breast:
30	chr1:149854077..149861961-chr1:150131511..150145996,30	MCF-7	breast:
31	chr1:149782512..149785665-chr1:149854381..149857469,5	MCF-7	breast:
32	chr1:149854392..149861957-chr1:150131544..150142194,21	K562	blood:
33	chr1:149854454..149857299-chr21:43097372..43099990,2	MCF-7	breast:
34	chr1:149854142..149859760-chr1:150182757..150186625,7	MCF-7	breast:

No data

Variant related genes	Relation type
BOLA1	TF binding region
HIST2H2AC	TF binding region
ENSG00000183558	Chromatin interaction
ENSG00000143401	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000261716	Chromatin interaction
ENSG00000259349	Chromatin interaction
ENSG00000178104	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000114859	Chromatin interaction
ENSG00000203819	Chromatin interaction
ENSG00000266187	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000136631	Chromatin interaction
ENSG00000272993	Chromatin interaction
ENSG00000170421	Chromatin interaction
ENSG00000203812	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000062725	Chromatin interaction
ENSG00000265451	Chromatin interaction
ENSG00000220323	Chromatin interaction
ENSG00000264229	Chromatin interaction
ENSG00000242663	Chromatin interaction
ENSG00000222222	Chromatin interaction
ENSG00000163113	Chromatin interaction
ENSG00000183598	Chromatin interaction
ENSG00000203814	Chromatin interaction
ENSG00000023902	Chromatin interaction
ENSG00000163882	Chromatin interaction
ENSG00000111057	Chromatin interaction
ENSG00000227702	Chromatin interaction
ENSG00000074054	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12087748	1.00[AMR][1000 genomes]
rs16837629	1.00[AMR][1000 genomes]
rs16837824	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16838897	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16841820	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59863517	0.83[AFR][1000 genomes]
rs61277719	1.00[AMR][1000 genomes]
rs61570934	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7518476	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	nsv432820	chr1:148921404-149920927	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	784 gene(s)	inside rSNPs	diseases
2	nsv831525	chr1:149701537-149878033	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
3	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149849200-149855800	Weak transcription	Right Atrium	heart
2	chr1:149851800-149855800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:149852000-149855800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:149853400-149856000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr1:149853600-149856200	Weak transcription	Pancreas	Pancrea
6	chr1:149854000-149856000	Weak transcription	Brain Angular Gyrus	brain
7	chr1:149854000-149856800	Weak transcription	Esophagus	oesophagus
8	chr1:149854800-149856000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr1:149854800-149856000	Enhancers	Psoas Muscle	Psoas
10	chr1:149854800-149856000	Weak transcription	NH-A	brain
11	chr1:149855000-149855800	Enhancers	Fetal Heart	heart
12	chr1:149855000-149856000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr1:149855000-149856000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:149855000-149856000	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr1:149855000-149856000	Enhancers	Liver	Liver
16	chr1:149855000-149856000	Flanking Active TSS	K562	blood
17	chr1:149855000-149856200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:149855000-149857400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr1:149855200-149855800	Enhancers	Primary hematopoietic stem cells	blood
20	chr1:149855200-149855800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:149855200-149855800	Enhancers	Fetal Intestine Large	intestine
22	chr1:149855200-149855800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr1:149855200-149855800	Flanking Active TSS	Thymus	Thymus
24	chr1:149855200-149855800	Enhancers	Hela-S3	cervix
25	chr1:149855200-149855800	Active TSS	Osteobl	bone
26	chr1:149855200-149856000	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr1:149855200-149856000	Enhancers	Brain Cingulate Gyrus	brain
28	chr1:149855200-149856000	Enhancers	Fetal Brain Male	brain
29	chr1:149855200-149856000	Genic enhancers	Fetal Intestine Small	intestine
30	chr1:149855200-149856000	Enhancers	Fetal Muscle Leg	muscle
31	chr1:149855200-149856000	Enhancers	Placenta	Placenta
32	chr1:149855200-149856000	Enhancers	Fetal Stomach	stomach
33	chr1:149855200-149856000	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr1:149855200-149856200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:149855200-149856200	Genic enhancers	Primary B cells from peripheral blood	blood
36	chr1:149855200-149856200	Enhancers	Primary T cells fromperipheralblood	blood
37	chr1:149855200-149856200	Enhancers	Colon Smooth Muscle	Colon
38	chr1:149855200-149856200	Enhancers	Left Ventricle	heart
39	chr1:149855200-149856400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:149855200-149856400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:149855200-149856400	Enhancers	Placenta Amnion	Placenta Amnion
42	chr1:149855200-149856400	Flanking Active TSS	GM12878-XiMat	blood
43	chr1:149855200-149856600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr1:149855200-149857000	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr1:149855200-149857600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:149855400-149855800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:149855400-149855800	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr1:149855400-149855800	Weak transcription	Right Ventricle	heart
49	chr1:149855400-149855800	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr1:149855400-149855800	Enhancers	A549	lung

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