Variant report

Variant	rs12598978
Chromosome Location	chr16:30482540-30482541
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:88)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:88 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT5A	chr16:30482124-30484576	GM12878	blood:	n/a	chr16:30483984-30483996 chr16:30483943-30483951
2	RUNX3	chr16:30481988-30485527	GM12878	blood:	n/a	n/a
3	BATF	chr16:30482307-30483333	GM12878	blood:	n/a	n/a
4	CHD1	chr16:30482210-30482604	GM12878	blood:	n/a	n/a
5	MEF2A	chr16:30481999-30482807	GM12878	blood:	n/a	n/a
6	MEF2A	chr16:30482115-30483305	GM12878	blood:	n/a	n/a
7	POU2F2	chr16:30482336-30482740	GM12891	blood:	n/a	n/a
8	BCL11A	chr16:30482181-30483351	GM12878	blood:	n/a	n/a
9	EBF1	chr16:30482217-30485580	GM12878	blood:	n/a	chr16:30485245-30485256 chr16:30485073-30485082
10	RELA	chr16:30482304-30482741	GM19099	blood:	n/a	n/a
11	PAX5	chr16:30482214-30482805	GM12878	blood:	n/a	n/a
12	STAT1	chr16:30482453-30482674	GM12878	blood:	n/a	n/a
13	STAT3	chr16:30482293-30482778	GM12878	blood:	n/a	n/a
14	POU2F2	chr16:30482179-30482877	GM12878	blood:	n/a	n/a
15	SP1	chr16:30482234-30482784	GM12878	blood:	n/a	n/a
16	ATF2	chr16:30482144-30482811	GM12878	blood:	n/a	n/a
17	BCL3	chr16:30482151-30482757	GM12878	blood:	n/a	n/a
18	RCOR1	chr16:30482195-30482675	GM12878	blood:	n/a	n/a
19	POLR2A	chr16:30482269-30482698	GM12892	blood:	n/a	n/a
20	IKZF1	chr16:30482185-30484365	GM12878	blood:	n/a	n/a
21	NFATC1	chr16:30482140-30483486	GM12878	blood:	n/a	n/a
22	CHD2	chr16:30482273-30482805	GM12878	blood:	n/a	n/a
23	TCF12	chr16:30482333-30482702	GM12878	blood:	n/a	n/a
24	BCL11A	chr16:30482337-30482703	GM12878	blood:	n/a	n/a
25	POLR2A	chr16:30482191-30482828	GM12892	blood:	n/a	n/a
26	YY1	chr16:30482068-30482678	GM12891	blood:	n/a	n/a
27	CEBPB	chr16:30482386-30482750	GM12878	blood:	n/a	n/a
28	NFIC	chr16:30482076-30483587	GM12878	blood:	n/a	n/a
29	POU2F2	chr16:30482124-30482714	GM12891	blood:	n/a	n/a
30	SPI1	chr16:30482351-30482685	GM12878	blood:	n/a	n/a
31	MTA3	chr16:30482146-30482781	GM12878	blood:	n/a	n/a
32	JUND	chr16:30482298-30482748	GM12878	blood:	n/a	n/a
33	EP300	chr16:30482177-30484201	GM12878	blood:	n/a	n/a
34	POU2F2	chr16:30482334-30482657	GM12878	blood:	n/a	n/a
35	FOXM1	chr16:30482060-30483574	GM12878	blood:	n/a	n/a
36	CEBPB	chr16:30482147-30483532	GM12878	blood:	n/a	n/a
37	TBP	chr16:30482270-30482830	GM12878	blood:	n/a	n/a
38	STAT5A	chr16:30482204-30482722	GM12878	blood:	n/a	n/a
39	EP300	chr16:30482220-30482845	GM12878	blood:	n/a	n/a
40	TCF3	chr16:30482309-30482766	GM12878	blood:	n/a	n/a
41	IRF4	chr16:30482327-30482879	GM12878	blood:	n/a	n/a
42	PML	chr16:30482322-30482699	GM12878	blood:	n/a	n/a
43	FOXM1	chr16:30482053-30483533	GM12878	blood:	n/a	n/a
44	TBL1XR1	chr16:30482174-30484289	GM12878	blood:	n/a	n/a
45	YY1	chr16:30482271-30482668	GM12878	blood:	n/a	n/a
46	BCLAF1	chr16:30482081-30482819	GM12878	blood:	n/a	n/a
47	PAX5	chr16:30482284-30482722	GM12891	blood:	n/a	n/a
48	BCLAF1	chr16:30482282-30482767	GM12878	blood:	n/a	n/a
49	BHLHE40	chr16:30482144-30483282	GM12878	blood:	n/a	n/a
50	POU2F2	chr16:30482238-30482710	GM12878	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30439379..30441756-chr16:30482330..30485596,3	K562	blood:
2	chr16:30478104..30482696-chr16:30483392..30486359,4	MCF-7	breast:
3	chr16:30455668..30458653-chr16:30481052..30482973,3	K562	blood:

No data

Variant related genes	Relation type
ITGAL	TF binding region
ENSG00000222701	TF binding region
ENSG00000179918	Chromatin interaction
ENSG00000005844	Chromatin interaction
ENSG00000179958	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11150589	1.00[ASW][hapmap];1.00[CEU][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];1.00[ASN][1000 genomes]
rs11574938	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11648955	0.93[ASN][1000 genomes]
rs12716977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12926510	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17839542	1.00[CHB][hapmap]
rs2285459	0.85[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs34686249	0.85[ASN][1000 genomes]
rs4630562	0.85[EUR][1000 genomes]
rs61598883	0.85[ASN][1000 genomes]
rs62056315	0.85[ASN][1000 genomes]
rs62056316	0.85[ASN][1000 genomes]
rs7186331	0.93[ASN][1000 genomes]
rs7196129	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7197010	0.86[EUR][1000 genomes]
rs8046842	0.93[ASN][1000 genomes]
rs8058719	0.86[ASN][1000 genomes]
rs8059970	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
2	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
4	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
5	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
6	nsv1783	chr16:30449450-30494321	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12598978	LOC645287	trans	multi-tissue	Pritchard
rs12598978	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30470600-30485000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:30477400-30483600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr16:30477600-30483000	Weak transcription	HepG2	liver
4	chr16:30479200-30483800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr16:30479400-30483400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr16:30479400-30484000	Weak transcription	Placenta	Placenta
7	chr16:30479600-30483200	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr16:30479800-30483400	Enhancers	Primary T cells fromperipheralblood	blood
9	chr16:30480200-30483600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr16:30480400-30483400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr16:30480400-30483400	Enhancers	Fetal Thymus	thymus
12	chr16:30480600-30482600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr16:30480600-30483000	Enhancers	Primary T cells from cord blood	blood
14	chr16:30480600-30483000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr16:30480600-30483000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr16:30480600-30483400	Enhancers	Primary B cells from cord blood	blood
17	chr16:30480600-30483400	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr16:30480600-30483600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr16:30480600-30483600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr16:30480600-30483800	Enhancers	Primary B cells from peripheral blood	blood
21	chr16:30481000-30483200	Enhancers	Thymus	Thymus
22	chr16:30481200-30483200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr16:30481600-30482600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr16:30481600-30483400	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr16:30481600-30483800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr16:30481800-30482600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr16:30481800-30482800	Enhancers	GM12878-XiMat	blood
28	chr16:30482000-30483400	Enhancers	Dnd41	blood
29	chr16:30482000-30483600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr16:30482000-30483800	Enhancers	Primary hematopoietic stem cells	blood
31	chr16:30482200-30483000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr16:30482400-30482600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr16:30482400-30483400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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