Variant report

Variant	rs59742045
Chromosome Location	chr1:84970750-84970751
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	JUN	chr1:84970079-84973077	K562	blood:	n/a	chr1:84970176-84970185 chr1:84972305-84972317 chr1:84972307-84972316
2	POLR2A	chr1:84969985-84972746	HCT-116	colon:	n/a	n/a
3	MXI1	chr1:84970410-84973047	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:84970344-84972750	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:84970407-84973119	GM19099	blood:	n/a	n/a
6	POLR2A	chr1:84970141-84972678	GM12892	blood:	n/a	n/a
7	TEAD4	chr1:84970725-84971356	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:84970276-84972805	Hela-S3	cervix:	n/a	n/a
9	PML	chr1:84970167-84973030	GM12878	blood:	n/a	n/a
10	EP300	chr1:84970209-84970940	GM12878	blood:	n/a	n/a
11	SMC3	chr1:84970269-84972875	Hela-S3	cervix:	n/a	chr1:84972211-84972219
12	TBP	chr1:84970234-84971496	Hela-S3	cervix:	n/a	n/a
13	NFATC1	chr1:84970321-84971066	GM12878	blood:	n/a	n/a
14	RCOR1	chr1:84970161-84972710	Hela-S3	cervix:	n/a	n/a
15	MXI1	chr1:84969756-84973236	IMR90	lung:	n/a	n/a
16	POLR2A	chr1:84957385-84973725	K562	blood:	n/a	n/a
17	NFIC	chr1:84970184-84970798	GM12878	blood:	n/a	n/a
18	RELA	chr1:84970322-84972863	GM18505	blood:	n/a	n/a
19	EBF1	chr1:84970370-84971572	GM12878	blood:	n/a	chr1:84970547-84970558
20	MYC	chr1:84970667-84972814	NB4	blood:	n/a	n/a
21	MAX	chr1:84970330-84972931	NB4	blood:	n/a	n/a
22	POLR2A	chr1:84970149-84973052	PBDE	blood:	n/a	n/a
23	RUNX3	chr1:84970121-84971121	GM12878	blood:	n/a	n/a
24	RELA	chr1:84970344-84972776	GM15510	blood:	n/a	n/a
25	POLR2A	chr1:84970263-84972827	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr1:84970011-84973130	IMR90	lung:	n/a	n/a
27	POLR2A	chr1:84970740-84972798	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr1:84970373-84972742	GM18951	blood:	n/a	n/a
29	IRF1	chr1:84970204-84970781	K562	blood:	n/a	chr1:84970207-84970224 chr1:84970212-84970223 chr1:84970574-84970590 chr1:84970766-84970780
30	POLR2A	chr1:84968320-84972670	HepG2	liver:	n/a	n/a
31	POLR2A	chr1:84970385-84972700	NB4	blood:	n/a	n/a
32	HCFC1	chr1:84970371-84973020	K562	blood:	n/a	n/a
33	MYBL2	chr1:84970654-84971452	HepG2	liver:	n/a	n/a
34	MAZ	chr1:84970275-84972915	K562	blood:	n/a	n/a
35	POLR2A	chr1:84970309-84972649	SK-N-SH	brain:	n/a	n/a
36	STAT1	chr1:84970401-84971502	GM12878	blood:	n/a	chr1:84971330-84971342
37	RELA	chr1:84970321-84972973	GM10847	blood:	n/a	n/a
38	POLR2A	chr1:84969408-84972646	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr1:84968524-84972839	PANC-1	pancreas:	n/a	n/a
40	MXI1	chr1:84970499-84972765	Hela-S3	cervix:	n/a	n/a
41	SIN3A	chr1:84970445-84972756	H1-hESC	embryonic stem cell:	n/a	chr1:84971562-84971573
42	POLR2A	chr1:84970247-84972855	GM18505	blood:	n/a	n/a
43	CEBPB	chr1:84970040-84972837	Hela-S3	cervix:	n/a	chr1:84971158-84971169 chr1:84971157-84971168 chr1:84971157-84971168 chr1:84971157-84971170 chr1:84971157-84971170
44	STAT3	chr1:84970409-84971102	GM12878	blood:	n/a	n/a
45	TBL1XR1	chr1:84970428-84971437	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:84970620-84972692	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr1:84970241-84972663	HL-60	blood:	n/a	n/a
48	POLR2A	chr1:84970161-84972450	SK-N-MC	brain:	n/a	n/a
49	POLR2A	chr1:84970177-84972658	GM12892	blood:	n/a	n/a
50	CHD1	chr1:84970703-84972929	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:84943777..84946552-chr1:84970497..84973179,2	MCF-7	breast:
2	chr1:84944684..84947410-chr1:84970225..84973395,6	MCF-7	breast:
3	chr1:84969735..84979623-chr1:84983174..84994888,16	K562	blood:
4	chr1:84543103..84544767-chr1:84969541..84972530,2	K562	blood:
5	chr1:84969596..84972494-chr1:85154864..85156849,3	K562	blood:
6	chr1:84966614..84978118-chr1:85034515..85041986,38	K562	blood:
7	chr1:84966967..84974535-chr1:85036439..85041823,24	K562	blood:
8	chr1:84970551..84971520-chr5:151151462..151152365,2	Hela-S3	cervix:

Variant related genes	Relation type
GNG5	TF binding region
SPATA1	TF binding region
ENSG00000177556	Chromatin interaction
ENSG00000117155	Chromatin interaction
ENSG00000271576	Chromatin interaction
ENSG00000145907	Chromatin interaction
ENSG00000142875	Chromatin interaction
ENSG00000117133	Chromatin interaction
ENSG00000117151	Chromatin interaction
ENSG00000122432	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11809752	1.00[AMR][1000 genomes]
rs57249159	1.00[AMR][1000 genomes]
rs57450857	1.00[AMR][1000 genomes]
rs72942047	1.00[AMR][1000 genomes]
rs72942059	1.00[AMR][1000 genomes]
rs72942078	1.00[AMR][1000 genomes]
rs72942082	1.00[AMR][1000 genomes]
rs72942100	1.00[AMR][1000 genomes]
rs72943903	1.00[AMR][1000 genomes]
rs72943915	1.00[AMR][1000 genomes]
rs72943959	1.00[AMR][1000 genomes]
rs72946340	1.00[AMR][1000 genomes]
rs72946347	1.00[AMR][1000 genomes]
rs72946374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 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	chr1:84946000-84970800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:84951200-84971000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:84968600-84970800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:84968600-84971400	Active TSS	Right Atrium	heart
5	chr1:84968800-84973200	Active TSS	Right Ventricle	heart
6	chr1:84969000-84970800	Transcr. at gene 5' and 3'	K562	blood
7	chr1:84969000-84973000	Active TSS	Left Ventricle	heart
8	chr1:84969200-84970800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr1:84969200-84970800	Flanking Active TSS	HMEC	breast
10	chr1:84969200-84970800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr1:84969200-84973200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:84969400-84970800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:84969400-84970800	Flanking Active TSS	Liver	Liver
14	chr1:84969400-84970800	Enhancers	Spleen	Spleen
15	chr1:84969400-84971200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr1:84969400-84971400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:84969400-84973200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:84969600-84970800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr1:84969600-84970800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:84969600-84970800	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr1:84969600-84971200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:84969800-84970800	Weak transcription	Gastric	stomach
23	chr1:84969800-84971000	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr1:84969800-84971000	Flanking Active TSS	Dnd41	blood
25	chr1:84969800-84973000	Active TSS	Muscle Satellite Cultured Cells	--
26	chr1:84969800-84973000	Active TSS	Aorta	Aorta
27	chr1:84969800-84973000	Active TSS	HSMM	muscle
28	chr1:84970000-84970800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr1:84970000-84971000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:84970000-84971000	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr1:84970000-84971000	Flanking Active TSS	Fetal Brain Female	brain
32	chr1:84970000-84971200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr1:84970000-84971200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:84970000-84972800	Active TSS	Ovary	ovary
35	chr1:84970000-84973000	Active TSS	Stomach Smooth Muscle	stomach
36	chr1:84970000-84973200	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr1:84970000-84973200	Active TSS	Fetal Intestine Large	intestine
38	chr1:84970000-84973600	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr1:84970000-84973600	Active TSS	GM12878-XiMat	blood
40	chr1:84970000-84973600	Active TSS	NHLF	lung
41	chr1:84970200-84970800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr1:84970200-84970800	Flanking Active TSS	Fetal Kidney	kidney
43	chr1:84970200-84971000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
44	chr1:84970200-84971000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr1:84970200-84971200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
46	chr1:84970200-84971200	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr1:84970200-84971200	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr1:84970200-84972800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:84970200-84972800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:84970200-84973000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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