Variant report

Variant	rs12486035
Chromosome Location	chr3:133916883-133916884
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	CTCF	chr3:133916740-133916890	WI-38	lung:	n/a	n/a
2	RAD21	chr3:133916435-133916945	HepG2	liver:	n/a	chr3:133916693-133916712
3	RAD21	chr3:133916521-133916901	HepG2	liver:	n/a	chr3:133916693-133916712
4	RAD21	chr3:133916354-133916999	MCF-7	breast:	n/a	chr3:133916693-133916712
5	CTCF	chr3:133916484-133916947	K562	blood:	n/a	chr3:133916693-133916709 chr3:133916694-133916715 chr3:133916692-133916710
6	SMC3	chr3:133916520-133916899	GM12878	blood:	n/a	chr3:133916694-133916708
7	RAD21	chr3:133916445-133916939	SK-N-SH_RA	brain:	n/a	chr3:133916693-133916712
8	GATA3	chr3:133916271-133917050	SK-N-SH	brain:	n/a	n/a
9	RAD21	chr3:133916447-133917064	ECC-1	luminal epithelium:	n/a	chr3:133916693-133916712
10	GATA2	chr3:133916413-133916905	HUVEC	blood vessel:	n/a	n/a
11	RAD21	chr3:133916522-133916915	GM12878	blood:	n/a	chr3:133916693-133916712
12	FOS	chr3:133916489-133916892	MCF10A-Er-Src	breast:	n/a	chr3:133916655-133916666 chr3:133916656-133916666 chr3:133916656-133916666 chr3:133916656-133916666
13	CTCF	chr3:133916428-133917018	A549	lung:	n/a	chr3:133916693-133916709 chr3:133916694-133916715 chr3:133916692-133916710
14	RFX5	chr3:133916510-133916896	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr3:133916760-133916910	A549	lung:	n/a	n/a
16	GATA3	chr3:133916307-133916968	SK-N-SH	brain:	n/a	n/a
17	RAD21	chr3:133916446-133917045	HCT-116	colon:	n/a	chr3:133916693-133916712
18	RAD21	chr3:133916435-133917004	HCT-116	colon:	n/a	chr3:133916693-133916712
19	CTCF	chr3:133916418-133916901	MCF-7	breast:	n/a	chr3:133916693-133916709 chr3:133916694-133916715 chr3:133916692-133916710
20	RAD21	chr3:133916436-133916982	ECC-1	luminal epithelium:	n/a	chr3:133916693-133916712
21	CTCF	chr3:133916493-133916997	MCF-7	breast:	n/a	chr3:133916693-133916709 chr3:133916694-133916715 chr3:133916692-133916710
22	FOS	chr3:133916542-133916892	MCF10A-Er-Src	breast:	n/a	chr3:133916655-133916666 chr3:133916656-133916666 chr3:133916656-133916666 chr3:133916656-133916666
23	CTCF	chr3:133916380-133917106	HCT-116	colon:	n/a	chr3:133916693-133916709 chr3:133916694-133916715 chr3:133916692-133916710
24	SMC3	chr3:133916425-133917140	SK-N-SH	brain:	n/a	chr3:133916694-133916708
25	SMC3	chr3:133916480-133916939	Hela-S3	cervix:	n/a	chr3:133916694-133916708
26	CTCF	chr3:133916482-133916930	GM12878	blood:	n/a	chr3:133916693-133916709 chr3:133916694-133916715 chr3:133916692-133916710
27	CTCF	chr3:133916338-133917152	SK-N-SH	brain:	n/a	chr3:133916693-133916709 chr3:133916694-133916715 chr3:133916692-133916710
28	FOSL2	chr3:133916414-133916913	MCF-7	breast:	n/a	chr3:133916656-133916666 chr3:133916656-133916666 chr3:133916656-133916666
29	RAD21	chr3:133916515-133916917	IMR90	lung:	n/a	chr3:133916693-133916712
30	CTCF	chr3:133916427-133916933	HCT-116	colon:	n/a	chr3:133916693-133916709 chr3:133916694-133916715 chr3:133916692-133916710
31	RAD21	chr3:133916428-133916893	H1-hESC	embryonic stem cell:	n/a	chr3:133916693-133916712
32	CTCF	chr3:133916564-133916893	A549	lung:	n/a	chr3:133916693-133916709 chr3:133916694-133916715 chr3:133916692-133916710
33	RAD21	chr3:133916500-133916944	Hela-S3	cervix:	n/a	chr3:133916693-133916712
34	GATA3	chr3:133916433-133916886	T-47D	breast:	n/a	n/a
35	CTCF	chr3:133916488-133916922	IMR90	lung:	n/a	chr3:133916693-133916709 chr3:133916694-133916715 chr3:133916692-133916710
36	RAD21	chr3:133916398-133917088	SK-N-SH	brain:	n/a	chr3:133916693-133916712
37	RAD21	chr3:133916473-133916892	H1-hESC	embryonic stem cell:	n/a	chr3:133916693-133916712
38	RAD21	chr3:133916386-133917038	A549	lung:	n/a	chr3:133916693-133916712
39	GATA1	chr3:133916014-133917092	PBDE	blood:	n/a	n/a
40	RAD21	chr3:133916470-133916927	A549	lung:	n/a	chr3:133916693-133916712
41	RAD21	chr3:133916435-133916930	MCF-7	breast:	n/a	chr3:133916693-133916712
42	RAD21	chr3:133916518-133916893	H1-hESC	embryonic stem cell:	n/a	chr3:133916693-133916712

No.	Distal block	Cell Line	Cell type
1	chr3:133916703..133918590-chr3:133919262..133920923,2	MCF-7	breast:
2	chr3:133916317..133917179-chr3:134198152..134199215,3	MCF-7	breast:
3	chr3:133916838..133918592-chr3:133930697..133932431,2	MCF-7	breast:
4	chr3:133915566..133917732-chr3:133929901..133931438,2	MCF-7	breast:
5	chr3:133916172..133917171-chr3:133930199..133931384,7	MCF-7	breast:
6	chr3:133916569..133917464-chr3:134395795..134396317,2	K562	blood:
7	chr3:133916227..133917047-chr3:133930033..133930914,2	K562	blood:

Variant related genes	Relation type
RYK	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10804626	1.00[CEU][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10804627	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10804628	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10804629	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10935098	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10935099	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10935100	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10935101	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10935102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10935105	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11914721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11922210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11925021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11927316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12485592	1.00[CEU][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487646	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12487925	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488092	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12488358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12491300	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12493904	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494030	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12494042	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12631354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs14533	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28648514	0.87[ASN][1000 genomes]
rs28883962	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28898351	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36077421	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4077106	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4077108	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4286404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4286405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4295144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4349494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4450813	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4453837	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4453838	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4505670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4588357	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58480012	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58703957	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59391701	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59839641	0.86[ASN][1000 genomes]
rs60202549	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60326170	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60545528	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60564425	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6439467	0.96[ASN][1000 genomes]
rs6439470	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs6439472	1.00[CEU][hapmap]
rs6776195	1.00[CEU][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6776260	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6783989	0.95[ASN][1000 genomes]
rs6791361	0.87[ASN][1000 genomes]
rs6800612	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7432230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7616326	0.87[ASN][1000 genomes]
rs7626278	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7631521	0.94[ASN][1000 genomes]
rs7646388	0.82[ASN][1000 genomes]
rs9883217	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs9884008	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133871800-133919200	Weak transcription	K562	blood
2	chr3:133874400-133929400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:133874600-133933600	Weak transcription	Colonic Mucosa	Colon
4	chr3:133877600-133935200	Weak transcription	Psoas Muscle	Psoas
5	chr3:133877800-133920200	Weak transcription	Brain Substantia Nigra	brain
6	chr3:133877800-133950200	Weak transcription	Small Intestine	intestine
7	chr3:133885600-133919600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:133888400-133923600	Weak transcription	Fetal Heart	heart
9	chr3:133893200-133917400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:133894800-133917800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:133894800-133917800	Weak transcription	Right Ventricle	heart
12	chr3:133894800-133917800	Weak transcription	Thymus	Thymus
13	chr3:133894800-133935200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:133894800-133946800	Weak transcription	Pancreas	Pancrea
15	chr3:133895000-133917200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:133895000-133917400	Weak transcription	Esophagus	oesophagus
17	chr3:133895000-133917800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:133895000-133918000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:133895000-133918000	Weak transcription	Spleen	Spleen
20	chr3:133895000-133918600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:133895000-133918800	Weak transcription	Aorta	Aorta
22	chr3:133895000-133950000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:133895000-133950200	Weak transcription	Gastric	stomach
24	chr3:133895200-133919600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:133895200-133927200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:133895600-133942800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:133895800-133923400	Weak transcription	Lung	lung
28	chr3:133898600-133919400	Weak transcription	A549	lung
29	chr3:133899000-133918000	Weak transcription	HSMMtube	muscle
30	chr3:133899000-133919200	Weak transcription	NHLF	lung
31	chr3:133899600-133919000	Weak transcription	Brain Germinal Matrix	brain
32	chr3:133899800-133918000	Weak transcription	Fetal Brain Female	brain
33	chr3:133900200-133918800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:133900800-133918000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:133901000-133918000	Weak transcription	Left Ventricle	heart
36	chr3:133902000-133919600	Weak transcription	Fetal Brain Male	brain
37	chr3:133902000-133930400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:133902600-133918200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:133902800-133919600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:133903000-133918000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:133903000-133929000	Weak transcription	GM12878-XiMat	blood
42	chr3:133903600-133919000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:133907400-133918600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:133907800-133918000	Weak transcription	Brain Anterior Caudate	brain
45	chr3:133907800-133927400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:133908000-133919400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:133909200-133918000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr3:133909200-133919200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:133909200-133920400	Weak transcription	Brain Angular Gyrus	brain
50	chr3:133909200-133943000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links