Variant report

Variant	rs12546492
Chromosome Location	chr8:103567976-103567977
allele	C/G
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	POLR2A	chr8:103567210-103568743	GM12892	blood:	n/a	n/a
2	YY1	chr8:103567346-103568232	GM12878	blood:	n/a	n/a
3	POLR2A	chr8:103567348-103568833	GM12892	blood:	n/a	n/a
4	SMC3	chr8:103567305-103568521	GM12878	blood:	n/a	chr8:103567433-103567440
5	RFX5	chr8:103567759-103568133	GM12878	blood:	n/a	n/a
6	POLR2A	chr8:103567628-103568357	GM12891	blood:	n/a	n/a
7	NFIC	chr8:103567391-103568206	GM12878	blood:	n/a	chr8:103567699-103567716
8	CTCF	chr8:103567920-103568070	GM12867	blood:	n/a	n/a
9	RCOR1	chr8:103567472-103568403	GM12878	blood:	n/a	n/a
10	ZNF143	chr8:103567372-103568230	GM12878	blood:	n/a	n/a
11	USF2	chr8:103567344-103568062	GM12878	blood:	n/a	n/a
12	EBF1	chr8:103567444-103568131	GM12878	blood:	n/a	n/a
13	CTCF	chr8:103567316-103568532	GM12878	blood:	n/a	chr8:103567363-103567384 chr8:103567370-103567383
14	RELA	chr8:103567419-103568537	GM18951	blood:	n/a	n/a
15	CTCF	chr8:103567880-103568030	GM12873	blood:	n/a	n/a
16	SP1	chr8:103567447-103568026	GM12878	blood:	n/a	chr8:103567896-103567909
17	POLR2A	chr8:103567381-103568689	GM12892	blood:	n/a	n/a
18	MAX	chr8:103567346-103568041	GM12878	blood:	n/a	n/a
19	POLR2A	chr8:103567535-103568531	GM12892	blood:	n/a	n/a
20	RUNX3	chr8:103567233-103568181	GM12878	blood:	n/a	n/a
21	POLR2A	chr8:103567434-103568647	GM18505	blood:	n/a	n/a
22	CTCF	chr8:103567922-103568045	K562	blood:	n/a	n/a
23	RELA	chr8:103567411-103568617	GM19099	blood:	n/a	n/a
24	CTCF	chr8:103567962-103568091	GM19238	blood:	n/a	n/a
25	RAD21	chr8:103567354-103568065	GM12878	blood:	n/a	chr8:103567366-103567385
26	RUNX3	chr8:103567407-103568330	GM12878	blood:	n/a	n/a
27	CTCF	chr8:103567860-103568010	GM12864	blood:	n/a	n/a
28	POLR2A	chr8:103567244-103568869	GM12878	blood:	n/a	n/a
29	BHLHE40	chr8:103567368-103568196	GM12878	blood:	n/a	n/a
30	MTA3	chr8:103567211-103568635	GM12878	blood:	n/a	n/a
31	ELK1	chr8:103567411-103568165	GM12878	blood:	n/a	n/a
32	CTCF	chr8:103567940-103568090	GM12878	blood:	n/a	n/a
33	SPI1	chr8:103567626-103568245	GM12878	blood:	n/a	n/a
34	EP300	chr8:103567493-103568477	GM12878	blood:	n/a	chr8:103568063-103568077 chr8:103567777-103567791
35	CHD2	chr8:103567476-103568216	GM12878	blood:	n/a	n/a
36	RELA	chr8:103567301-103568654	GM12891	blood:	n/a	n/a
37	ATF2	chr8:103567386-103568250	GM12878	blood:	n/a	n/a
38	NFATC1	chr8:103567384-103568344	GM12878	blood:	n/a	chr8:103567413-103567427
39	MTA3	chr8:103567153-103568687	GM12878	blood:	n/a	n/a
40	RELA	chr8:103567379-103568464	GM18526	blood:	n/a	n/a
41	POLR2A	chr8:103567359-103568656	GM12878	blood:	n/a	n/a
42	BCLAF1	chr8:103567397-103568172	GM12878	blood:	n/a	n/a
43	POLR2A	chr8:103567331-103568682	GM12878	blood:	n/a	n/a
44	STAT5A	chr8:103567452-103568204	GM12878	blood:	n/a	chr8:103568008-103568020
45	RELA	chr8:103567442-103568246	GM12892	blood:	n/a	n/a
46	NFIC	chr8:103567322-103568656	GM12878	blood:	n/a	chr8:103567699-103567716
47	CTCF	chr8:103567940-103568090	GM12872	blood:	n/a	n/a
48	CTCF	chr8:103567960-103568110	GM12864	blood:	n/a	n/a
49	TBL1XR1	chr8:103567385-103568047	GM12878	blood:	n/a	n/a
50	POLR2A	chr8:103567718-103568206	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:103566130..103569047-chr8:103588313..103590545,3	MCF-7	breast:
2	chr8:103567304..103569694-chr8:103578366..103580055,2	MCF-7	breast:

Variant related genes	Relation type
ODF1	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11990360	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2289032	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3808357	0.87[ASN][1000 genomes]
rs58139425	0.88[ASN][1000 genomes]
rs62523271	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7011180	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs998201	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1031769	chr8:103460754-103620283	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv539703	chr8:103460754-103620283	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv2762761	chr8:103492356-103625244	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv1831575	chr8:103498317-103585093	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1838972	chr8:103498317-103585093	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1024876	chr8:103512785-103576658	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3419415	chr8:103525141-103575507	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv534151	chr8:103563857-103589862	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103550800-103589000	Weak transcription	Right Atrium	heart
2	chr8:103554000-103569000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr8:103557000-103569200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr8:103557200-103582000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr8:103565800-103568200	Enhancers	GM12878-XiMat	blood
6	chr8:103566600-103568000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr8:103566600-103569000	Weak transcription	K562	blood
8	chr8:103566600-103576000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr8:103567400-103570000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr8:103567600-103568400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr8:103567800-103568000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr8:103567800-103568400	Enhancers	Duodenum Mucosa	Duodenum
13	chr8:103567800-103568800	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links