Variant report

Variant	rs16906575
Chromosome Location	chr10:52366563-52366564
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	CEBPB	chr10:52366386-52366569	HepG2	liver:	n/a	chr10:52366483-52366494
2	RCOR1	chr10:52366406-52366799	K562	blood:	n/a	n/a
3	ARID3A	chr10:52366335-52366645	HepG2	liver:	n/a	n/a
4	FOXA1	chr10:52366261-52366682	T-47D	breast:	n/a	n/a
5	JUND	chr10:52366400-52366625	HepG2	liver:	n/a	chr10:52366519-52366528
6	EP300	chr10:52366394-52366577	K562	blood:	n/a	chr10:52366498-52366508
7	MAFK	chr10:52366512-52366675	K562	blood:	n/a	chr10:52366625-52366642
8	JUN	chr10:52362653-52366775	K562	blood:	n/a	chr10:52366484-52366497 chr10:52363911-52363922 chr10:52366515-52366528 chr10:52366519-52366528
9	FOXA1	chr10:52366354-52366752	HepG2	liver:	n/a	n/a
10	BHLHE40	chr10:52366358-52366636	HepG2	liver:	n/a	n/a
11	CEBPB	chr10:52365772-52366680	HepG2	liver:	n/a	chr10:52366483-52366494
12	JUN	chr10:52366312-52366732	HepG2	liver:	n/a	chr10:52366484-52366497 chr10:52366515-52366528 chr10:52366519-52366528
13	FOXA1	chr10:52366349-52366690	HepG2	liver:	n/a	n/a
14	JUN	chr10:52366381-52366651	K562	blood:	n/a	chr10:52366484-52366497 chr10:52366515-52366528 chr10:52366519-52366528
15	FOS	chr10:52366335-52366670	MCF10A-Er-Src	breast:	n/a	chr10:52366519-52366528
16	FOXA2	chr10:52366355-52366686	A549	lung:	n/a	n/a
17	CEBPB	chr10:52365982-52366674	K562	blood:	n/a	chr10:52366483-52366494
18	FOXA1	chr10:52366319-52366668	T-47D	breast:	n/a	n/a
19	SP1	chr10:52366241-52366813	A549	lung:	n/a	n/a
20	MXI1	chr10:52366358-52366621	HepG2	liver:	n/a	n/a
21	FOS	chr10:52366345-52366584	MCF10A-Er-Src	breast:	n/a	chr10:52366519-52366528
22	CEBPB	chr10:52365859-52366832	A549	lung:	n/a	chr10:52366483-52366494 chr10:52366670-52366682
23	CEBPB	chr10:52365930-52366689	K562	blood:	n/a	chr10:52366483-52366494 chr10:52366670-52366682
24	FOXA2	chr10:52366375-52366607	HepG2	liver:	n/a	n/a
25	GATA3	chr10:52366289-52366703	T-47D	breast:	n/a	n/a
26	GATA3	chr10:52366344-52366694	T-47D	breast:	n/a	n/a
27	CUX1	chr10:52366345-52366679	K562	blood:	n/a	n/a
28	FOS	chr10:52366347-52366636	MCF10A-Er-Src	breast:	n/a	chr10:52366519-52366528
29	CEBPB	chr10:52365989-52366684	Hela-S3	cervix:	n/a	chr10:52366483-52366494 chr10:52366670-52366682
30	CEBPB	chr10:52365990-52366673	HepG2	liver:	n/a	chr10:52366483-52366494
31	CEBPB	chr10:52365986-52366673	IMR90	lung:	n/a	chr10:52366483-52366494
32	ATF3	chr10:52366330-52366714	A549	lung:	n/a	chr10:52366520-52366527 chr10:52366519-52366530 chr10:52366517-52366530 chr10:52366516-52366531 chr10:52366519-52366527 chr10:52366520-52366530
33	RFX5	chr10:52366558-52366758	K562	blood:	n/a	n/a
34	CREB1	chr10:52366264-52366736	HepG2	liver:	n/a	chr10:52366517-52366530
35	ATF3	chr10:52366329-52366662	K562	blood:	n/a	chr10:52366520-52366527 chr10:52366519-52366530 chr10:52366517-52366530 chr10:52366516-52366531 chr10:52366519-52366527 chr10:52366520-52366530
36	FOXA1	chr10:52366346-52366692	HepG2	liver:	n/a	n/a
37	CEBPB	chr10:52366367-52366692	A549	lung:	n/a	chr10:52366483-52366494 chr10:52366670-52366682
38	TEAD4	chr10:52366225-52366746	HepG2	liver:	n/a	chr10:52366692-52366701
39	CEBPB	chr10:52366279-52366732	MCF-7	breast:	n/a	chr10:52366483-52366494 chr10:52366670-52366682
40	JUND	chr10:52366304-52366682	Hela-S3	cervix:	n/a	chr10:52366519-52366528
41	ZNF384	chr10:52366500-52367089	K562	blood:	n/a	n/a
42	FOXA1	chr10:52366336-52366672	HepG2	liver:	n/a	n/a
43	JUND	chr10:52366311-52366736	HepG2	liver:	n/a	chr10:52366519-52366528
44	ATF1	chr10:52366344-52366675	K562	blood:	n/a	n/a
45	JUND	chr10:52366334-52366654	K562	blood:	n/a	chr10:52366519-52366528
46	CEBPB	chr10:52365979-52366696	A549	lung:	n/a	chr10:52366483-52366494 chr10:52366670-52366682
47	FOXA2	chr10:52366313-52366746	A549	lung:	n/a	n/a
48	CREB1	chr10:52366281-52366731	HepG2	liver:	n/a	chr10:52366517-52366530
49	TBL1XR1	chr10:52366410-52366580	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:52356810..52366659-chr10:52378806..52385975,25	MCF-7	breast:
2	chr10:52358660..52367648-chr10:52378481..52386533,25	MCF-7	breast:
3	chr10:52365691..52371767-chr10:52381261..52385919,7	K562	blood:

Variant related genes	Relation type
ENSG00000230036	TF binding region
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10508930	0.82[GIH][hapmap]
rs12241969	1.00[EUR][1000 genomes]
rs12267258	1.00[EUR][1000 genomes]
rs12571898	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12572578	0.85[CHB][hapmap];1.00[EUR][1000 genomes]
rs16907261	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4615973	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55703887	1.00[EUR][1000 genomes]
rs55928478	1.00[EUR][1000 genomes]
rs56039956	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57040666	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57073115	1.00[EUR][1000 genomes]
rs57238750	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs57253864	1.00[EUR][1000 genomes]
rs57574235	1.00[EUR][1000 genomes]
rs57871603	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60613759	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60974974	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61027189	1.00[EUR][1000 genomes]
rs61518314	1.00[EUR][1000 genomes]
rs61615406	1.00[EUR][1000 genomes]
rs7080895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7083978	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7093159	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73318780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73320893	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73320899	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74131448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7908759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52338000-52367000	Weak transcription	Aorta	Aorta
2	chr10:52341200-52373000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr10:52358400-52367000	Enhancers	Fetal Lung	lung
4	chr10:52358800-52367800	Enhancers	Brain Hippocampus Middle	brain
5	chr10:52359400-52369200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr10:52360200-52375600	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr10:52361600-52369000	Enhancers	Brain Anterior Caudate	brain
8	chr10:52362000-52368400	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr10:52362000-52368400	Enhancers	Brain Substantia Nigra	brain
10	chr10:52362200-52367400	Enhancers	Brain Cingulate Gyrus	brain
11	chr10:52362200-52372400	Weak transcription	Esophagus	oesophagus
12	chr10:52362400-52367200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr10:52362600-52366800	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr10:52362600-52368800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr10:52362800-52368000	Enhancers	HepG2	liver
16	chr10:52363000-52368000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr10:52363200-52368000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:52363200-52368000	Enhancers	Stomach Mucosa	stomach
19	chr10:52363200-52371600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr10:52363200-52372000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr10:52363400-52368000	Enhancers	Colon Smooth Muscle	Colon
22	chr10:52363800-52366600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr10:52363800-52367800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr10:52364000-52367200	Enhancers	Right Ventricle	heart
25	chr10:52364000-52367600	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr10:52364000-52369800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr10:52364200-52368400	Enhancers	Duodenum Mucosa	Duodenum
28	chr10:52364200-52370000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr10:52364400-52372000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr10:52364400-52374400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr10:52365000-52366600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr10:52365000-52366600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr10:52365000-52366600	Enhancers	HMEC	breast
34	chr10:52365000-52368800	Enhancers	Fetal Heart	heart
35	chr10:52365000-52368800	Weak transcription	Thymus	Thymus
36	chr10:52365000-52369800	Weak transcription	Gastric	stomach
37	chr10:52365000-52369800	Weak transcription	Right Atrium	heart
38	chr10:52365000-52371000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr10:52365200-52366800	Enhancers	NHEK	skin
40	chr10:52365200-52367000	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr10:52365200-52367600	Enhancers	NHLF	lung
42	chr10:52365200-52368200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr10:52365200-52368200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr10:52365200-52369600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr10:52365200-52374000	Weak transcription	Placenta	Placenta
46	chr10:52365400-52366600	Enhancers	Stomach Smooth Muscle	stomach
47	chr10:52365400-52366800	Weak transcription	Fetal Stomach	stomach
48	chr10:52365400-52366800	Weak transcription	Psoas Muscle	Psoas
49	chr10:52365400-52367200	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr10:52365400-52367400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links