Variant report

Variant	rs17679370
Chromosome Location	chr2:177796823-177796824
allele	C/T
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	BATF	chr2:177796434-177796932	GM12878	blood:	n/a	chr2:177796714-177796725
2	FOXM1	chr2:177796458-177797429	GM12878	blood:	n/a	n/a
3	EP300	chr2:177796551-177796909	Hela-S3	cervix:	n/a	chr2:177796649-177796663 chr2:177796650-177796664 chr2:177796718-177796727 chr2:177796655-177796669 chr2:177796717-177796726 chr2:177796819-177796833 chr2:177796653-177796667
4	STAT1	chr2:177796596-177796962	GM12878	blood:	n/a	chr2:177796717-177796726 chr2:177796824-177796835 chr2:177796718-177796727
5	NFATC1	chr2:177796351-177797053	GM12878	blood:	n/a	n/a
6	TCF12	chr2:177796612-177797216	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:177796705-177797033	GM12891	blood:	n/a	n/a
8	CHD2	chr2:177796441-177797400	GM12878	blood:	n/a	n/a
9	YY1	chr2:177796688-177796991	GM12878	blood:	n/a	n/a
10	RFX5	chr2:177796358-177797054	GM12878	blood:	n/a	n/a
11	FOS	chr2:177796574-177796900	Hela-S3	cervix:	n/a	chr2:177796718-177796726 chr2:177796717-177796726 chr2:177796718-177796725 chr2:177796718-177796727
12	CEBPD	chr2:177796547-177797005	K562	blood:	n/a	n/a
13	FOSL2	chr2:177796445-177796927	A549	lung:	n/a	chr2:177796718-177796726 chr2:177796717-177796726 chr2:177796718-177796725 chr2:177796718-177796727
14	UBTF	chr2:177796697-177797009	K562	blood:	n/a	n/a
15	ATF2	chr2:177796384-177797229	GM12878	blood:	n/a	n/a
16	RAD21	chr2:177796503-177796964	GM12878	blood:	n/a	n/a
17	JUND	chr2:177796412-177796999	HCT-116	colon:	n/a	chr2:177796718-177796726 chr2:177796717-177796726 chr2:177796718-177796725 chr2:177796718-177796727 chr2:177796716-177796727
18	STAT5A	chr2:177796467-177797234	GM12878	blood:	n/a	chr2:177796717-177796726 chr2:177796824-177796835 chr2:177796718-177796727
19	TEAD4	chr2:177796483-177797006	ECC-1	luminal epithelium:	n/a	n/a
20	GATA3	chr2:177796668-177796846	SH-SY5Y	brain:	n/a	n/a
21	POLR2A	chr2:177796784-177796957	GM12878	blood:	n/a	n/a
22	JUN	chr2:177796571-177796886	K562	blood:	n/a	chr2:177796718-177796726 chr2:177796717-177796726 chr2:177796718-177796725 chr2:177796718-177796727
23	ELK1	chr2:177796677-177797323	GM12878	blood:	n/a	n/a
24	PAX5	chr2:177796479-177797140	GM12878	blood:	n/a	chr2:177796824-177796833
25	MYC	chr2:177796553-177797278	K562	blood:	n/a	chr2:177796718-177796727
26	CUX1	chr2:177796246-177797318	GM12878	blood:	n/a	n/a
27	BCL11A	chr2:177796534-177796995	GM12878	blood:	n/a	chr2:177796718-177796727 chr2:177796824-177796833 chr2:177796717-177796726
28	EBF1	chr2:177796428-177797288	GM12878	blood:	n/a	n/a
29	CEBPB	chr2:177796529-177796940	K562	blood:	n/a	n/a
30	MAX	chr2:177796542-177797301	GM12878	blood:	n/a	chr2:177796718-177796727
31	CEBPB	chr2:177796323-177797256	GM12878	blood:	n/a	n/a
32	BATF	chr2:177796465-177797037	GM12878	blood:	n/a	chr2:177796714-177796725
33	TCF3	chr2:177796747-177796983	GM12878	blood:	n/a	n/a
34	BHLHE40	chr2:177796454-177798272	GM12878	blood:	n/a	chr2:177797165-177797174 chr2:177797158-177797179
35	RUNX3	chr2:177796332-177797349	GM12878	blood:	n/a	n/a
36	CTCF	chr2:177796680-177796830	GM12872	blood:	n/a	chr2:177796698-177796714
37	GATA3	chr2:177796579-177796962	MCF-7	breast:	n/a	n/a
38	POLR2A	chr2:177796738-177796977	GM12891	blood:	n/a	n/a
39	KAP1	chr2:177796438-177797154	HEK293	kidney:	n/a	chr2:177796719-177796728 chr2:177796716-177796725
40	JUN	chr2:177796598-177796865	HepG2	liver:	n/a	chr2:177796718-177796726 chr2:177796717-177796726 chr2:177796718-177796725 chr2:177796718-177796727
41	FOS	chr2:177796491-177796944	HUVEC	blood vessel:	n/a	chr2:177796718-177796726 chr2:177796717-177796726 chr2:177796718-177796725 chr2:177796718-177796727
42	EP300	chr2:177796530-177797049	GM12878	blood:	n/a	chr2:177796649-177796663 chr2:177796650-177796664 chr2:177796718-177796727 chr2:177796655-177796669 chr2:177796717-177796726 chr2:177796819-177796833 chr2:177796653-177796667
43	TCF7L2	chr2:177796554-177797123	HEK293	kidney:	n/a	chr2:177796718-177796727
44	POLR2A	chr2:177794408-177803203	K562	blood:	n/a	n/a
45	BHLHE40	chr2:177796521-177797395	K562	blood:	n/a	chr2:177797165-177797174 chr2:177797158-177797179
46	MYC	chr2:177796595-177797247	K562	blood:	n/a	chr2:177796718-177796727
47	NFATC1	chr2:177796323-177797188	GM12878	blood:	n/a	n/a
48	GATA3	chr2:177796637-177796878	T-47D	breast:	n/a	n/a
49	MEF2A	chr2:177796358-177797215	GM12878	blood:	n/a	n/a
50	UBTF	chr2:177796756-177796881	K562	blood:	n/a	n/a

Variant related genes	Relation type
RNU6-187P	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10186950	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930766	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930772	1.00[ASN][1000 genomes]
rs12469347	1.00[JPT][hapmap]
rs12612709	1.00[ASN][1000 genomes]
rs12616782	1.00[JPT][hapmap]
rs13005005	1.00[JPT][hapmap]
rs13421731	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13422461	1.00[ASN][1000 genomes]
rs1355845	1.00[JPT][hapmap]
rs1355854	0.90[ASN][1000 genomes]
rs1398967	0.90[ASN][1000 genomes]
rs1398969	0.90[ASN][1000 genomes]
rs1398977	0.90[ASN][1000 genomes]
rs1405614	0.90[ASN][1000 genomes]
rs1513870	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1527265	1.00[ASN][1000 genomes]
rs1527266	1.00[ASN][1000 genomes]
rs16864736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866134	1.00[JPT][hapmap]
rs2196658	0.82[ASN][1000 genomes]
rs2696966	1.00[ASN][1000 genomes]
rs4894207	0.90[ASN][1000 genomes]
rs61177850	0.90[ASN][1000 genomes]
rs6433618	0.90[ASN][1000 genomes]
rs6433624	1.00[ASN][1000 genomes]
rs6707899	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6710025	1.00[ASN][1000 genomes]
rs6760271	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7562938	0.90[ASN][1000 genomes]
rs7588841	1.00[JPT][hapmap]
rs840698	1.00[JPT][hapmap]
rs840699	1.00[JPT][hapmap]

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	nsv875448	chr2:177760005-177819108	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv875449	chr2:177775612-177835010	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv875450	chr2:177785155-177819108	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17679370	OLA1	cis	parietal	SCAN
rs17679370	NFE2L2	cis	parietal	SCAN
rs17679370	OSBPL6	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:177795200-177797000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:177796000-177797000	Enhancers	Primary T cells fromperipheralblood	blood
3	chr2:177796000-177797000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:177796200-177797400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr2:177796200-177798200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:177796400-177797000	Active TSS	GM12878-XiMat	blood
7	chr2:177796400-177797000	Enhancers	Hela-S3	cervix
8	chr2:177796600-177797000	Enhancers	H9 Cell Line	embryonic stem cell
9	chr2:177796600-177797000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:177796600-177797000	Enhancers	Fetal Heart	heart
11	chr2:177796600-177797000	Enhancers	HSMM	muscle
12	chr2:177796800-177797000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr2:177796800-177797000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:177796800-177797000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:177796800-177797000	Flanking Active TSS	K562	blood
16	chr2:177796800-177797200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr2:177796800-177797200	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr2:177796800-177797200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:177796800-177797400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr2:177796800-177797400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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