Variant report

Variant	rs6502546
Chromosome Location	chr17:16878488-16878489
allele	A/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	chr17:16878230-16880821	GM12878	blood:	n/a	n/a
2	RUNX3	chr17:16878190-16879379	GM12878	blood:	n/a	n/a
3	STAT1	chr17:16878472-16878516	GM12878	blood:	n/a	n/a
4	PBX3	chr17:16878339-16878564	GM12878	blood:	n/a	chr17:16878482-16878491
5	MAZ	chr17:16878412-16879990	GM12878	blood:	n/a	n/a
6	MTA3	chr17:16878010-16881023	GM12878	blood:	n/a	n/a
7	IKZF1	chr17:16878253-16880127	GM12878	blood:	n/a	n/a
8	FOXM1	chr17:16878167-16880028	GM12878	blood:	n/a	n/a
9	POLR2A	chr17:16878427-16879927	GM12878	blood:	n/a	n/a
10	MEF2A	chr17:16878361-16879330	GM12878	blood:	n/a	chr17:16878837-16878851
11	MTA3	chr17:16878127-16880599	GM12878	blood:	n/a	n/a
12	NFIC	chr17:16878293-16880132	GM12878	blood:	n/a	n/a
13	POU2F2	chr17:16878209-16879025	GM12878	blood:	n/a	n/a
14	POLR2A	chr17:16878342-16880680	GM18505	blood:	n/a	n/a
15	RELA	chr17:16878366-16880312	GM12878	blood:	n/a	n/a
16	STAT3	chr17:16878466-16880603	GM12878	blood:	n/a	chr17:16879276-16879288 chr17:16879889-16879900
17	BHLHE40	chr17:16878364-16880280	GM12878	blood:	n/a	n/a
18	CUX1	chr17:16878126-16879966	GM12878	blood:	n/a	n/a
19	NFATC1	chr17:16878386-16880024	GM12878	blood:	n/a	n/a
20	EP300	chr17:16878390-16880675	GM12878	blood:	n/a	chr17:16879297-16879311 chr17:16879298-16879312
21	POLR2A	chr17:16878056-16880305	GM12892	blood:	n/a	n/a
22	CHD1	chr17:16878240-16880652	GM12878	blood:	n/a	n/a
23	SMC3	chr17:16878404-16879110	GM12878	blood:	n/a	n/a
24	POLR2A	chr17:16878086-16880910	GM12892	blood:	n/a	n/a
25	EP300	chr17:16878282-16880413	GM12878	blood:	n/a	chr17:16879297-16879311 chr17:16879298-16879312
26	POLR2A	chr17:16878062-16880885	GM12878	blood:	n/a	n/a
27	POLR2A	chr17:16877924-16880892	GM12892	blood:	n/a	n/a
28	WRNIP1	chr17:16878277-16879886	GM12878	blood:	n/a	n/a
29	NFIC	chr17:16878245-16880801	GM12878	blood:	n/a	n/a
30	EBF1	chr17:16878282-16880926	GM12878	blood:	n/a	chr17:16879702-16879713
31	PML	chr17:16878377-16880180	GM12878	blood:	n/a	n/a
32	ATF2	chr17:16878391-16879183	GM12878	blood:	n/a	n/a
33	POLR2A	chr17:16878302-16880573	GM12891	blood:	n/a	n/a
34	POLR2A	chr17:16878138-16878926	GM12892	blood:	n/a	n/a
35	TBP	chr17:16878380-16880770	GM12878	blood:	n/a	n/a
36	MEF2A	chr17:16878288-16880050	GM12878	blood:	n/a	chr17:16878837-16878851
37	ATF2	chr17:16878298-16880053	GM12878	blood:	n/a	n/a
38	FOXA1	chr17:16878260-16878508	T-47D	breast:	n/a	chr17:16878412-16878424
39	CHD2	chr17:16878225-16879969	GM12878	blood:	n/a	n/a
40	RCOR1	chr17:16878383-16880321	GM12878	blood:	n/a	n/a
41	BCLAF1	chr17:16878367-16880024	GM12878	blood:	n/a	n/a
42	CEBPB	chr17:16878432-16880095	GM12878	blood:	n/a	n/a
43	MXI1	chr17:16878465-16880743	GM12878	blood:	n/a	n/a
44	IRF4	chr17:16878454-16879963	GM12878	blood:	n/a	n/a
45	RELA	chr17:16878335-16879959	GM19099	blood:	n/a	n/a
46	RUNX3	chr17:16878306-16880030	GM12878	blood:	n/a	n/a
47	FOXM1	chr17:16878248-16880298	GM12878	blood:	n/a	n/a
48	STAT5A	chr17:16877948-16880337	GM12878	blood:	n/a	chr17:16879276-16879288 chr17:16878439-16878451

Variant related genes	Relation type
TNFRSF13B	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11078362	0.94[ASN][1000 genomes]
rs12601542	0.94[ASN][1000 genomes]
rs35196703	0.81[ASN][1000 genomes]
rs35898095	0.81[ASN][1000 genomes]
rs4985758	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7212800	0.81[ASN][1000 genomes]
rs7501462	0.97[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	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv2761948	chr17:16868561-16920568	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr17:16867400-16883800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:16873000-16880800	Enhancers	Fetal Thymus	thymus
3	chr17:16874200-16880000	Enhancers	Dnd41	blood
4	chr17:16875200-16885800	Enhancers	Primary B cells from cord blood	blood
5	chr17:16875600-16878600	Weak transcription	Thymus	Thymus
6	chr17:16875800-16887200	Enhancers	Primary B cells from peripheral blood	blood
7	chr17:16877400-16879600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr17:16878000-16878600	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr17:16878000-16882800	Flanking Active TSS	GM12878-XiMat	blood
10	chr17:16878200-16878800	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr17:16878200-16879200	Enhancers	Brain Germinal Matrix	brain
12	chr17:16878400-16880600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr17:16878400-16883600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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