Variant report

Variant	rs16864736
Chromosome Location	chr2:177796683-177796684
allele	G/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	STAT3	chr2:177796592-177796819	MCF10A-Er-Src	breast:	n/a	chr2:177796717-177796726 chr2:177796718-177796727
4	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
5	STAT1	chr2:177796596-177796962	GM12878	blood:	n/a	chr2:177796717-177796726 chr2:177796824-177796835 chr2:177796718-177796727
6	CTCF	chr2:177796580-177796730	GM12872	blood:	n/a	chr2:177796698-177796714
7	NFATC1	chr2:177796351-177797053	GM12878	blood:	n/a	n/a
8	TCF12	chr2:177796612-177797216	GM12878	blood:	n/a	n/a
9	CHD2	chr2:177796441-177797400	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	ATF2	chr2:177796384-177797229	GM12878	blood:	n/a	n/a
15	RAD21	chr2:177796503-177796964	GM12878	blood:	n/a	n/a
16	JUND	chr2:177796412-177796999	HCT-116	colon:	n/a	chr2:177796718-177796726 chr2:177796717-177796726 chr2:177796718-177796725 chr2:177796718-177796727 chr2:177796716-177796727
17	STAT5A	chr2:177796467-177797234	GM12878	blood:	n/a	chr2:177796717-177796726 chr2:177796824-177796835 chr2:177796718-177796727
18	TEAD4	chr2:177796483-177797006	ECC-1	luminal epithelium:	n/a	n/a
19	GATA3	chr2:177796668-177796846	SH-SY5Y	brain:	n/a	n/a
20	JUN	chr2:177796571-177796886	K562	blood:	n/a	chr2:177796718-177796726 chr2:177796717-177796726 chr2:177796718-177796725 chr2:177796718-177796727
21	ELK1	chr2:177796677-177797323	GM12878	blood:	n/a	n/a
22	PAX5	chr2:177796479-177797140	GM12878	blood:	n/a	chr2:177796824-177796833
23	MYC	chr2:177796553-177797278	K562	blood:	n/a	chr2:177796718-177796727
24	CUX1	chr2:177796246-177797318	GM12878	blood:	n/a	n/a
25	BCL11A	chr2:177796534-177796995	GM12878	blood:	n/a	chr2:177796718-177796727 chr2:177796824-177796833 chr2:177796717-177796726
26	EBF1	chr2:177796428-177797288	GM12878	blood:	n/a	n/a
27	CEBPB	chr2:177796529-177796940	K562	blood:	n/a	n/a
28	MAX	chr2:177796542-177797301	GM12878	blood:	n/a	chr2:177796718-177796727
29	CEBPB	chr2:177796323-177797256	GM12878	blood:	n/a	n/a
30	BATF	chr2:177796465-177797037	GM12878	blood:	n/a	chr2:177796714-177796725
31	BHLHE40	chr2:177796454-177798272	GM12878	blood:	n/a	chr2:177797165-177797174 chr2:177797158-177797179
32	RUNX3	chr2:177796332-177797349	GM12878	blood:	n/a	n/a
33	CTCF	chr2:177796680-177796830	GM12872	blood:	n/a	chr2:177796698-177796714
34	GATA3	chr2:177796579-177796962	MCF-7	breast:	n/a	n/a
35	KAP1	chr2:177796438-177797154	HEK293	kidney:	n/a	chr2:177796719-177796728 chr2:177796716-177796725
36	JUN	chr2:177796598-177796865	HepG2	liver:	n/a	chr2:177796718-177796726 chr2:177796717-177796726 chr2:177796718-177796725 chr2:177796718-177796727
37	FOS	chr2:177796491-177796944	HUVEC	blood vessel:	n/a	chr2:177796718-177796726 chr2:177796717-177796726 chr2:177796718-177796725 chr2:177796718-177796727
38	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
39	TCF7L2	chr2:177796554-177797123	HEK293	kidney:	n/a	chr2:177796718-177796727
40	CTCF	chr2:177796660-177796810	RPTEC	kidney:	n/a	chr2:177796698-177796714
41	POLR2A	chr2:177794408-177803203	K562	blood:	n/a	n/a
42	HMGN3	chr2:177796596-177796795	K562	blood:	n/a	n/a
43	BHLHE40	chr2:177796521-177797395	K562	blood:	n/a	chr2:177797165-177797174 chr2:177797158-177797179
44	MYC	chr2:177796595-177797247	K562	blood:	n/a	chr2:177796718-177796727
45	NFATC1	chr2:177796323-177797188	GM12878	blood:	n/a	n/a
46	CEBPB	chr2:177796599-177796810	K562	blood:	n/a	n/a
47	GATA3	chr2:177796637-177796878	T-47D	breast:	n/a	n/a
48	MEF2A	chr2:177796358-177797215	GM12878	blood:	n/a	n/a
49	SP1	chr2:177796438-177797145	GM12878	blood:	n/a	n/a
50	TCF12	chr2:177796418-177796916	MCF-7	breast:	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	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930766	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[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]
rs17628074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17679370	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]
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
rs16864736	OSBPL6	cis	cerebellum	SCAN
rs16864736	NFE2L2	cis	parietal	SCAN
rs16864736	OLA1	cis	parietal	SCAN

Chromatin state (count:15 , 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	chr2:177796400-177796800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:177796400-177797000	Active TSS	GM12878-XiMat	blood
8	chr2:177796400-177797000	Enhancers	Hela-S3	cervix
9	chr2:177796600-177796800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr2:177796600-177796800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:177796600-177796800	Active TSS	K562	blood
12	chr2:177796600-177797000	Enhancers	H9 Cell Line	embryonic stem cell
13	chr2:177796600-177797000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:177796600-177797000	Enhancers	Fetal Heart	heart
15	chr2:177796600-177797000	Enhancers	HSMM	muscle

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