Variant report

Variant	rs35124447
Chromosome Location	chr3:46538569-46538570
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr3:46538082-46538615	K562	blood:	n/a	n/a
2	RAD21	chr3:46538257-46538610	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr3:46538134-46538744	SK-N-SH	brain:	n/a	n/a
4	RAD21	chr3:46538263-46538574	IMR90	lung:	n/a	n/a
5	CTCF	chr3:46538302-46538607	H1-hESC	embryonic stem cell:	n/a	n/a
6	RCOR1	chr3:46537241-46539044	IMR90	lung:	n/a	n/a
7	RAD21	chr3:46538089-46538689	HCT-116	colon:	n/a	n/a
8	PAX5	chr3:46538295-46538610	GM12878	blood:	n/a	n/a
9	CTCF	chr3:46538356-46538570	GM12891	blood:	n/a	n/a
10	RCOR1	chr3:46538262-46538670	K562	blood:	n/a	n/a
11	BHLHE40	chr3:46538379-46538583	K562	blood:	n/a	n/a
12	CTCF	chr3:46538119-46538734	K562	blood:	n/a	n/a
13	CTCF	chr3:46538189-46538610	K562	blood:	n/a	n/a
14	RAD21	chr3:46538194-46538676	HCT-116	colon:	n/a	n/a
15	RAD21	chr3:46538292-46538599	GM12878	blood:	n/a	n/a
16	MAFK	chr3:46538405-46538626	K562	blood:	n/a	n/a
17	CTCF	chr3:46538058-46538830	SK-N-SH	brain:	n/a	n/a
18	CTCF	chr3:46538209-46538627	K562	blood:	n/a	n/a
19	ZNF143	chr3:46538269-46538594	K562	blood:	n/a	n/a
20	JUND	chr3:46538257-46538613	K562	blood:	n/a	n/a
21	CUX1	chr3:46538326-46538623	K562	blood:	n/a	n/a
22	CTCF	chr3:46538440-46538590	HVMF	connective:	n/a	n/a
23	ZC3H11A	chr3:46538399-46538624	K562	blood:	n/a	n/a
24	CTCF	chr3:46538197-46538601	K562	blood:	n/a	n/a
25	RAD21	chr3:46538306-46538575	GM12878	blood:	n/a	n/a
26	CTCF	chr3:46538297-46538609	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr3:46538303-46538674	MCF-7	breast:	n/a	n/a
28	CTCF	chr3:46538234-46538589	IMR90	lung:	n/a	n/a
29	RAD21	chr3:46538271-46538610	GM12878	blood:	n/a	n/a
30	ZNF143	chr3:46538315-46538583	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr3:46538130-46538768	HCT-116	colon:	n/a	n/a
32	ATF1	chr3:46538294-46538577	K562	blood:	n/a	n/a
33	RAD21	chr3:46538293-46538654	H1-hESC	embryonic stem cell:	n/a	n/a
34	RAD21	chr3:46538283-46538579	HepG2	liver:	n/a	n/a
35	SMC3	chr3:46538239-46538588	GM12878	blood:	n/a	n/a
36	ZNF143	chr3:46538260-46538574	GM12878	blood:	n/a	n/a
37	RAD21	chr3:46538223-46538689	H1-hESC	embryonic stem cell:	n/a	n/a
38	SMC3	chr3:46538184-46538787	SK-N-SH	brain:	n/a	n/a
39	ZNF384	chr3:46538319-46538579	K562	blood:	n/a	n/a
40	TBL1XR1	chr3:46538340-46538625	K562	blood:	n/a	n/a
41	CTCF	chr3:46538230-46538619	GM12878	blood:	n/a	n/a
42	RAD21	chr3:46538174-46538656	ECC-1	luminal epithelium:	n/a	n/a
43	CTCF	chr3:46538183-46538678	MCF-7	breast:	n/a	n/a
44	REST	chr3:46538341-46538695	K562	blood:	n/a	n/a
45	PAX5	chr3:46538322-46538600	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46537971..46538930-chr3:46599529..46600154,4	MCF-7	breast:

No data

Variant related genes	Relation type
RTP3	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs13061783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13070959	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13076697	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13077283	0.88[ASN][1000 genomes]
rs13083022	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13093282	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099992	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13353428	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17078930	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17286758	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28539486	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28595844	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28617572	0.89[EUR][1000 genomes]
rs28670418	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28687398	0.88[EUR][1000 genomes]
rs34167705	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34227041	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34668230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34767161	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34850133	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35056755	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35082490	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35740565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35760835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35864396	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3934895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55689943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55702201	0.87[ASN][1000 genomes]
rs56106816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56288081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442003	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6442004	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66627456	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66702674	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66826527	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67091203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67222447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67228693	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67305272	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67647205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769817	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6770016	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770574	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6772291	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6778305	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6778415	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6778422	0.90[ASN][1000 genomes]
rs6783443	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6792420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67962987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801427	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804179	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68095529	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71622507	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73067779	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73069915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73069952	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7624932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625793	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7626061	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7628435	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7648827	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9808967	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9846026	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9865911	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9866206	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9867359	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9871405	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014624	chr3:46463424-46549188	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1009892	chr3:46496775-46546918	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv536553	chr3:46496775-46546918	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46530800-46538600	Weak transcription	Pancreas	Pancrea
2	chr3:46531200-46541600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:46531400-46540200	Weak transcription	Left Ventricle	heart
4	chr3:46533000-46544200	Weak transcription	Psoas Muscle	Psoas
5	chr3:46535000-46538600	Weak transcription	Fetal Intestine Large	intestine
6	chr3:46537200-46538600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr3:46537200-46538600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr3:46537200-46538600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:46537200-46538600	Enhancers	NH-A	brain
10	chr3:46537200-46538600	Enhancers	NHDF-Ad	bronchial
11	chr3:46537200-46538800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr3:46537200-46538800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:46537200-46538800	Enhancers	Osteobl	bone
14	chr3:46537200-46539000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr3:46537200-46539000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr3:46537200-46539200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:46537200-46540000	Enhancers	Dnd41	blood
18	chr3:46537200-46546200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:46537200-46547000	Enhancers	Fetal Thymus	thymus
20	chr3:46537200-46550200	Enhancers	K562	blood
21	chr3:46537400-46538800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:46537400-46539000	Enhancers	HUVEC	blood vessel
23	chr3:46537400-46539600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:46537400-46542000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:46537600-46538800	Enhancers	Right Atrium	heart
26	chr3:46537600-46539400	Enhancers	Adipose Nuclei	Adipose
27	chr3:46538000-46538800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:46538000-46538800	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr3:46538000-46538800	Enhancers	Fetal Heart	heart
30	chr3:46538000-46539200	Enhancers	Primary B cells from peripheral blood	blood
31	chr3:46538000-46539600	Enhancers	Primary T cells from cord blood	blood
32	chr3:46538000-46542200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:46538200-46539600	Weak transcription	HSMMtube	muscle
34	chr3:46538200-46540000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:46538200-46541600	Weak transcription	HSMM	muscle
36	chr3:46538200-46542000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr3:46538200-46546800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:46538400-46538600	Enhancers	Primary T cells fromperipheralblood	blood
39	chr3:46538400-46538600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr3:46538400-46538800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
41	chr3:46538400-46538800	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr3:46538400-46538800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr3:46538400-46538800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:46538400-46538800	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr3:46538400-46538800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:46538400-46538800	Enhancers	Thymus	Thymus
47	chr3:46538400-46539000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:46538400-46539000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
49	chr3:46538400-46539000	Enhancers	Lung	lung
50	chr3:46538400-46539200	Enhancers	Primary T helper cells fromperipheralblood	blood

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