Variant report

Variant	rs6502547
Chromosome Location	chr17:16878657-16878658
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	POLR2A	chr17:16878579-16878775	GM12878	blood:	n/a	n/a
2	ZNF143	chr17:16878651-16878758	GM12878	blood:	n/a	n/a
3	POLR2A	chr17:16878230-16880821	GM12878	blood:	n/a	n/a
4	MEF2C	chr17:16878543-16879272	GM12878	blood:	n/a	chr17:16878837-16878851
5	RUNX3	chr17:16878190-16879379	GM12878	blood:	n/a	n/a
6	TBL1XR1	chr17:16878505-16880241	GM12878	blood:	n/a	n/a
7	TCF12	chr17:16878588-16878997	GM12878	blood:	n/a	n/a
8	RFX5	chr17:16878552-16879400	GM12878	blood:	n/a	n/a
9	MAZ	chr17:16878412-16879990	GM12878	blood:	n/a	n/a
10	MTA3	chr17:16878010-16881023	GM12878	blood:	n/a	n/a
11	IKZF1	chr17:16878253-16880127	GM12878	blood:	n/a	n/a
12	FOXM1	chr17:16878167-16880028	GM12878	blood:	n/a	n/a
13	POLR2A	chr17:16878427-16879927	GM12878	blood:	n/a	n/a
14	MEF2A	chr17:16878361-16879330	GM12878	blood:	n/a	chr17:16878837-16878851
15	MTA3	chr17:16878127-16880599	GM12878	blood:	n/a	n/a
16	NFIC	chr17:16878293-16880132	GM12878	blood:	n/a	n/a
17	BCL3	chr17:16878541-16879107	GM12878	blood:	n/a	n/a
18	POU2F2	chr17:16878209-16879025	GM12878	blood:	n/a	n/a
19	POLR2A	chr17:16878342-16880680	GM18505	blood:	n/a	n/a
20	RELA	chr17:16878366-16880312	GM12878	blood:	n/a	n/a
21	STAT3	chr17:16878466-16880603	GM12878	blood:	n/a	chr17:16879276-16879288 chr17:16879889-16879900
22	POLR2A	chr17:16878552-16878868	GM12891	blood:	n/a	n/a
23	BHLHE40	chr17:16878364-16880280	GM12878	blood:	n/a	n/a
24	TCF12	chr17:16878571-16879009	GM12878	blood:	n/a	n/a
25	POLR2A	chr17:16878546-16878954	GM12891	blood:	n/a	n/a
26	CUX1	chr17:16878126-16879966	GM12878	blood:	n/a	n/a
27	NFATC1	chr17:16878386-16880024	GM12878	blood:	n/a	n/a
28	EBF1	chr17:16878510-16879933	GM12878	blood:	n/a	chr17:16879702-16879713
29	EP300	chr17:16878390-16880675	GM12878	blood:	n/a	chr17:16879297-16879311 chr17:16879298-16879312
30	BCL11A	chr17:16878517-16879010	GM12878	blood:	n/a	n/a
31	POLR2A	chr17:16878056-16880305	GM12892	blood:	n/a	n/a
32	CHD1	chr17:16878240-16880652	GM12878	blood:	n/a	n/a
33	PML	chr17:16878518-16878963	GM12878	blood:	n/a	n/a
34	SMC3	chr17:16878404-16879110	GM12878	blood:	n/a	n/a
35	POLR2A	chr17:16878086-16880910	GM12892	blood:	n/a	n/a
36	EP300	chr17:16878282-16880413	GM12878	blood:	n/a	chr17:16879297-16879311 chr17:16879298-16879312
37	POLR2A	chr17:16878062-16880885	GM12878	blood:	n/a	n/a
38	PAX5	chr17:16878559-16879047	GM12878	blood:	n/a	n/a
39	EBF1	chr17:16878504-16879327	GM12878	blood:	n/a	n/a
40	POLR2A	chr17:16878537-16878799	GM12891	blood:	n/a	n/a
41	POLR2A	chr17:16877924-16880892	GM12892	blood:	n/a	n/a
42	WRNIP1	chr17:16878277-16879886	GM12878	blood:	n/a	n/a
43	NFIC	chr17:16878245-16880801	GM12878	blood:	n/a	n/a
44	BCL11A	chr17:16878608-16879017	GM12878	blood:	n/a	n/a
45	BATF	chr17:16878509-16879015	GM12878	blood:	n/a	n/a
46	EBF1	chr17:16878282-16880926	GM12878	blood:	n/a	chr17:16879702-16879713
47	POLR2A	chr17:16878617-16880545	GM12878	blood:	n/a	n/a
48	ZNF384	chr17:16878540-16879824	GM12878	blood:	n/a	n/a
49	STAT5A	chr17:16878599-16879970	GM12878	blood:	n/a	chr17:16879276-16879288
50	PML	chr17:16878377-16880180	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16864871..16867780-chr17:16878608..16880115,2	MCF-7	breast:

Variant related genes	Relation type
TNFRSF13B	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs4075606	1.00[ASN][1000 genomes]
rs4985757	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985762	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502545	0.89[AFR][1000 genomes]
rs6502548	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7220753	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7503780	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7504096	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv543230	chr17:16878578-16892465	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 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	chr17:16875800-16887200	Enhancers	Primary B cells from peripheral blood	blood
6	chr17:16877400-16879600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr17:16878000-16882800	Flanking Active TSS	GM12878-XiMat	blood
8	chr17:16878200-16878800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr17:16878200-16879200	Enhancers	Brain Germinal Matrix	brain
10	chr17:16878400-16880600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr17:16878400-16883600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr17:16878600-16878800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr17:16878600-16878800	Enhancers	Duodenum Mucosa	Duodenum
14	chr17:16878600-16879000	Bivalent Enhancer	HSMMtube	muscle
15	chr17:16878600-16880200	Enhancers	Thymus	Thymus
16	chr17:16878600-16881600	Weak transcription	Rectal Mucosa Donor 29	rectum

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