Variant report

Variant	rs10875882
Chromosome Location	chr12:49260691-49260692
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	EP300	chr12:49260681-49261110	HepG2	liver:	n/a	chr12:49260760-49260774 chr12:49260754-49260768 chr12:49260879-49260889
2	FOXA1	chr12:49260691-49261242	HepG2	liver:	n/a	chr12:49260942-49260957
3	TCF12	chr12:49260685-49261155	A549	lung:	n/a	n/a
4	CREB1	chr12:49260605-49261169	HepG2	liver:	n/a	n/a
5	NR3C1	chr12:49260660-49261263	A549	lung:	n/a	n/a
6	NFIC	chr12:49260625-49261165	HepG2	liver:	n/a	n/a
7	FOSL2	chr12:49260681-49261222	HepG2	liver:	n/a	n/a
8	GATA3	chr12:49260594-49261202	A549	lung:	n/a	chr12:49260833-49260844
9	CREB1	chr12:49260678-49261133	HepG2	liver:	n/a	n/a
10	BCL3	chr12:49260639-49261168	A549	lung:	n/a	n/a
11	FOXA1	chr12:49260644-49261107	T-47D	breast:	n/a	chr12:49260942-49260957
12	MYBL2	chr12:49260683-49261270	HepG2	liver:	n/a	n/a
13	USF1	chr12:49260611-49261134	A549	lung:	n/a	n/a
14	FOXA1	chr12:49260668-49261252	HepG2	liver:	n/a	chr12:49260942-49260957
15	FOXA2	chr12:49260486-49261223	A549	lung:	n/a	n/a
16	USF1	chr12:49260622-49261160	A549	lung:	n/a	n/a
17	EP300	chr12:49260678-49261184	HepG2	liver:	n/a	chr12:49260760-49260774 chr12:49260754-49260768 chr12:49260879-49260889
18	ELF1	chr12:49260674-49261190	MCF-7	breast:	n/a	n/a
19	MAX	chr12:49260647-49261156	MCF-7	breast:	n/a	chr12:49261040-49261051
20	GATA3	chr12:49260603-49261207	A549	lung:	n/a	chr12:49260833-49260844
21	TCF12	chr12:49260587-49261250	A549	lung:	n/a	n/a
22	EGR1	chr12:49260622-49261139	MCF-7	breast:	n/a	n/a
23	USF1	chr12:49260590-49261178	A549	lung:	n/a	n/a
24	USF1	chr12:49260686-49261085	HepG2	liver:	n/a	n/a
25	EP300	chr12:49260678-49261103	T-47D	breast:	n/a	chr12:49260760-49260774 chr12:49260754-49260768 chr12:49260879-49260889
26	MYBL2	chr12:49260655-49261207	HepG2	liver:	n/a	n/a
27	EP300	chr12:49260563-49261350	A549	lung:	n/a	chr12:49260760-49260774 chr12:49260754-49260768 chr12:49260879-49260889
28	USF1	chr12:49260659-49260990	A549	lung:	n/a	n/a
29	FOSL2	chr12:49260610-49261270	A549	lung:	n/a	n/a
30	EP300	chr12:49260662-49261245	A549	lung:	n/a	chr12:49260760-49260774 chr12:49260754-49260768 chr12:49260879-49260889
31	FOXA1	chr12:49260683-49261089	HepG2	liver:	n/a	chr12:49260942-49260957
32	MAX	chr12:49260590-49261218	A549	lung:	n/a	chr12:49261040-49261051
33	SP1	chr12:49260553-49261254	A549	lung:	n/a	chr12:49260699-49260706
34	FOXA2	chr12:49260595-49261284	A549	lung:	n/a	n/a
35	SP1	chr12:49260617-49261184	HepG2	liver:	n/a	chr12:49260699-49260706
36	HDAC2	chr12:49260645-49261125	HepG2	liver:	n/a	chr12:49260759-49260773 chr12:49260753-49260767 chr12:49260880-49260889 chr12:49261052-49261060 chr12:49260761-49260775
37	ATF3	chr12:49260681-49261155	A549	lung:	n/a	n/a
38	USF1	chr12:49260548-49261163	A549	lung:	n/a	n/a
39	TEAD4	chr12:49260595-49261138	HepG2	liver:	n/a	n/a
40	BCL3	chr12:49260582-49261199	A549	lung:	n/a	n/a
41	REST	chr12:49260582-49261263	A549	lung:	n/a	chr12:49260735-49260755 chr12:49260735-49260755
42	JUND	chr12:49260621-49261289	A549	lung:	n/a	n/a
43	JUND	chr12:49260653-49261234	A549	lung:	n/a	n/a
44	ELF1	chr12:49260689-49261177	A549	lung:	n/a	n/a
45	SP1	chr12:49260571-49261304	A549	lung:	n/a	chr12:49260699-49260706
46	ATF3	chr12:49260591-49261105	A549	lung:	n/a	n/a
47	MAX	chr12:49260604-49261204	A549	lung:	n/a	chr12:49261040-49261051

No.	Distal block	Cell Line	Cell type
1	chr12:49109119..49112520-chr12:49258264..49261147,4	MCF-7	breast:
2	chr12:49245526..49248872-chr12:49257959..49262254,6	K562	blood:
3	chr12:49253202..49256104-chr12:49256944..49260973,5	K562	blood:
4	chr12:49216573..49218418-chr12:49258019..49261488,3	MCF-7	breast:
5	chr12:49210034..49212452-chr12:49258517..49260819,2	MCF-7	breast:
6	chr12:49244737..49248613-chr12:49256890..49261439,8	MCF-7	breast:
7	chr12:49207497..49209388-chr12:49258268..49261041,2	MCF-7	breast:
8	chr12:49259749..49262409-chr12:49343841..49346815,2	MCF-7	breast:
9	chr12:49217911..49220873-chr12:49258155..49260990,2	K562	blood:
10	chr12:49259911..49262225-chr12:49462450..49464634,2	MCF-7	breast:
11	chr12:49207073..49210037-chr12:49258262..49262278,4	MCF-7	breast:
12	chr12:49257454..49260772-chr12:49317154..49320539,3	MCF-7	breast:
13	chr12:49258480..49261342-chr12:49348804..49351192,2	MCF-7	breast:

Variant related genes	Relation type
RND1	TF binding region
ENSG00000167550	Chromatin interaction
ENSG00000134285	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000129315	Chromatin interaction
ENSG00000172602	Chromatin interaction
ENSG00000134287	Chromatin interaction
ENSG00000272822	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10783285	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1565933	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2446972	0.94[ASN][1000 genomes]
rs3759148	0.88[ASN][1000 genomes]
rs3782360	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760597	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760598	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760599	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4760639	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv469373	chr12:49256792-49285390	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
2	nsv558832	chr12:49256792-49285390	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
3	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49259800-49261000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:49259800-49261200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:49259800-49266600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:49260000-49261000	Enhancers	Duodenum Mucosa	Duodenum
5	chr12:49260000-49261000	Enhancers	Pancreas	Pancrea
6	chr12:49260000-49261000	Enhancers	HMEC	breast
7	chr12:49260000-49261800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:49260200-49260800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:49260200-49261000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr12:49260200-49261000	Enhancers	H1 Cell Line	embryonic stem cell
11	chr12:49260200-49261000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr12:49260200-49261000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr12:49260200-49261000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:49260200-49261000	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr12:49260200-49261000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr12:49260200-49261000	Enhancers	Osteobl	bone
17	chr12:49260200-49261200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr12:49260200-49261800	Enhancers	Adipose Nuclei	Adipose
19	chr12:49260200-49262000	Weak transcription	K562	blood
20	chr12:49260200-49263200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:49260200-49263200	Weak transcription	Fetal Lung	lung
22	chr12:49260200-49265000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:49260400-49261000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr12:49260600-49261000	Flanking Active TSS	Liver	Liver
25	chr12:49260600-49261000	Flanking Active TSS	Stomach Mucosa	stomach
26	chr12:49260600-49261000	Flanking Active TSS	HepG2	liver
27	chr12:49260600-49261600	Flanking Active TSS	A549	lung

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