Variant report

Variant	rs6690277
Chromosome Location	chr1:154553437-154553438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154552586-154553958	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:154549138-154553602	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:154548361-154553602	K562	blood:	n/a	n/a
4	POLR2A	chr1:154548085-154554030	GM12891	blood:	n/a	n/a
5	POLR2A	chr1:154553266-154553583	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:154553287-154553530	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:154553266-154553553	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:154553286-154553619	GM12891	blood:	n/a	n/a
9	POLR2A	chr1:154546928-154553519	Hela-S3	cervix:	n/a	n/a
10	NFATC1	chr1:154553282-154553689	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:154547840-154554530	GM12892	blood:	n/a	n/a
12	POLR2A	chr1:154553300-154553502	K562	blood:	n/a	n/a
13	POLR2A	chr1:154553274-154553593	H1-neurons	neurons:	n/a	n/a
14	POLR2A	chr1:154553260-154553509	K562	blood:	n/a	n/a
15	POLR2A	chr1:154547114-154553910	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:154546848-154554115	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:154549169-154554048	GM12892	blood:	n/a	n/a
18	POLR2A	chr1:154551396-154554078	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:154553386-154553538	GM12878	blood:	n/a	n/a
20	PML	chr1:154553289-154553772	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:154553234-154554016	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr1:154546809-154553884	GM12891	blood:	n/a	n/a
23	POLR2A	chr1:154551564-154554008	GM12891	blood:	n/a	n/a
24	POLR2A	chr1:154549198-154554105	GM12892	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154530666..154532588-chr1:154552871..154554473,2	MCF-7	breast:
2	chr1:154550052..154552028-chr1:154552192..154555232,3	K562	blood:
3	chr1:154521062..154522565-chr1:154552295..154555132,2	K562	blood:
4	chr1:154552762..154554449-chr1:154556991..154558544,2	MCF-7	breast:
5	chr1:154552595..154555534-chr1:154570614..154573461,2	K562	blood:
6	chr1:154552368..154554542-chr1:154578229..154579744,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000233875	TF binding region
ENSG00000160710	Chromatin interaction
ENSG00000160714	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11264221	0.88[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11264231	0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs11264232	0.83[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs11806816	0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs12079381	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs12086987	0.83[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12090237	1.00[MEX][hapmap]
rs12092890	0.81[LWK][hapmap]
rs12094866	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1542796	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2172708	0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6677920	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6683149	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7513474	0.82[AFR][1000 genomes]
rs9427095	0.95[YRI][hapmap];0.94[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	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154545400-154561800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:154547800-154578400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:154548000-154555200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:154548000-154571800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:154548200-154575400	Strong transcription	Fetal Brain Female	brain
6	chr1:154548800-154575400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:154548800-154577400	Strong transcription	Fetal Intestine Small	intestine
8	chr1:154549200-154575800	Strong transcription	Brain Germinal Matrix	brain
9	chr1:154549400-154572200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:154549400-154575400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:154549400-154576200	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:154549400-154576200	Strong transcription	Primary T cells from cord blood	blood
13	chr1:154549400-154578000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:154549600-154572000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:154549600-154575200	Strong transcription	Fetal Intestine Large	intestine
16	chr1:154549600-154576400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:154549800-154576400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:154549800-154576800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:154550000-154553600	Weak transcription	Hela-S3	cervix
20	chr1:154550000-154556400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:154550000-154570600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:154550000-154571000	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr1:154550000-154571400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:154550000-154574600	Strong transcription	A549	lung
25	chr1:154550200-154571800	Strong transcription	Fetal Thymus	thymus
26	chr1:154550200-154575200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:154550200-154575200	Strong transcription	Placenta Amnion	Placenta Amnion
28	chr1:154550200-154576200	Strong transcription	Thymus	Thymus
29	chr1:154550200-154576400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:154550400-154557200	Strong transcription	GM12878-XiMat	blood
31	chr1:154550400-154566200	Strong transcription	Primary hematopoietic stem cells	blood
32	chr1:154550400-154566200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:154550400-154567800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:154550400-154571000	Strong transcription	Brain Hippocampus Middle	brain
35	chr1:154550400-154571400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:154550400-154571800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:154550400-154576200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
38	chr1:154550600-154555600	Strong transcription	HUVEC	blood vessel
39	chr1:154550600-154556400	Strong transcription	NHLF	lung
40	chr1:154550600-154564800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:154550600-154566000	Strong transcription	Gastric	stomach
42	chr1:154550600-154571200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:154550600-154571200	Strong transcription	Osteobl	bone
44	chr1:154550600-154571800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:154550600-154572000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:154550600-154572200	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr1:154550600-154572200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:154550600-154575200	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr1:154550600-154576000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr1:154550800-154553600	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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