Variant report

Variant	rs4499252
Chromosome Location	chr16:31538982-31538983
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr16:31538935-31539268	K562	blood:	n/a	n/a
2	POLR2A	chr16:31538948-31539296	K562	blood:	n/a	n/a
3	TEAD4	chr16:31538951-31539266	K562	blood:	n/a	n/a
4	NR2F2	chr16:31538954-31539313	K562	blood:	n/a	n/a
5	ZNF384	chr16:31538851-31539291	K562	blood:	n/a	n/a
6	TAL1	chr16:31538906-31539385	K562	blood:	n/a	n/a
7	ARID3A	chr16:31538858-31539290	K562	blood:	n/a	n/a
8	GATA1	chr16:31538912-31539303	PBDEFetal	blood:	n/a	chr16:31539013-31539021
9	ELF1	chr16:31538805-31539185	K562	blood:	n/a	n/a
10	EP300	chr16:31538914-31539296	K562	blood:	n/a	chr16:31539055-31539069 chr16:31539053-31539067 chr16:31539062-31539076 chr16:31539061-31539075 chr16:31539059-31539073 chr16:31539060-31539074
11	IRF1	chr16:31538915-31539566	K562	blood:	n/a	chr16:31539384-31539393
12	CEBPB	chr16:31538903-31539060	K562	blood:	n/a	n/a
13	POLR2A	chr16:31538823-31542665	PBDE	blood:	n/a	n/a
14	GATA1	chr16:31538429-31539850	PBDE	blood:	n/a	chr16:31538750-31538760 chr16:31539013-31539021 chr16:31538751-31538760
15	NR2F2	chr16:31538859-31539335	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:31538946-31538996	GM12878	blood:	n/a
2	chr16:31538946-31538996	HRE	kidney:	n/a
3	chr16:31538946-31538996	AG04450	lung:	fetal
4	chr16:31538946-31538996	SK-N-SH	brain:	n/a
5	chr16:31538946-31538996	GM19239	blood:	n/a
6	chr16:31538946-31538996	HL-60	blood:	n/a
7	chr16:31538946-31538996	HMEC	breast:	n/a
8	chr16:31538946-31538996	HEK293	kidney:	embryo
9	chr16:31538946-31538996	HAEpiC	amniotic membrane:	n/a
10	chr16:31538946-31538996	HEEpiC	esophagus:	n/a
11	chr16:31538946-31538996	NHDF-neo	bronchial:	n/a
12	chr16:31538946-31538996	SK-N-SH_RA	brain:	n/a
13	chr16:31538946-31538996	ovcar-3	ovarian:	n/a
14	chr16:31538946-31538996	HCPEpiC	choroid plexus:	n/a
15	chr16:31538946-31538996	NT2-D1	testis:	n/a
16	chr16:31538946-31538996	MCF-7	breast:	n/a
17	chr16:31538946-31538996	Hela-S3	cervix:	n/a
18	chr16:31538946-31538996	K562	blood:	n/a
19	chr16:31538946-31538996	Jurkat	blood:	n/a
20	chr16:31538946-31538996	HNPCEpiC	eye:	n/a
21	chr16:31538946-31538996	AoSMC	blood vessel:	n/a
22	chr16:31538946-31538996	PrEC	prostate:	n/a
23	chr16:31538946-31538996	HCF	heart:	n/a
24	chr16:31538946-31538996	GM12892	blood:	n/a
25	chr16:31538946-31538996	PFSK-1	brain:	n/a
26	chr16:31538946-31538996	MCF10A-Er-Src	breast:	n/a
27	chr16:31538946-31538996	AG04449	skin:	fetal
28	chr16:31538946-31538996	AG09319	gingival:	n/a
29	chr16:31538946-31538996	SAEC	small airway:	n/a
30	chr16:31538946-31538996	HPAEpiC	pulmonary alveolar:	n/a
31	chr16:31538946-31538996	GM06990	blood:	n/a
32	chr16:31538946-31538996	SK-N-MC	brain:	n/a
33	chr16:31538946-31538996	HUVEC	blood vessel:	n/a
34	chr16:31538946-31538996	HepG2	liver:	n/a
35	chr16:31538946-31538996	HRPEpiC	eye:	n/a
36	chr16:31538946-31538996	BE2_C	brain:	n/a
37	chr16:31538946-31538996	U87	brain:	n/a
38	chr16:31538946-31538996	HIPEpiC	eye:	n/a
39	chr16:31538946-31538996	IMR90	lung:	fetal
40	chr16:31538946-31538996	SKMC	muscle:	n/a
41	chr16:31538946-31538996	HCT-116	colon:	n/a
42	chr16:31538946-31538996	BJ	skin:	n/a
43	chr16:31538946-31538996	NH-A	brain:	n/a
44	chr16:31538946-31538996	Hepatocyte	liver:	n/a
45	chr16:31538946-31538996	GM12891	blood:	n/a
46	chr16:31538946-31538996	NB4	blood:	n/a
47	chr16:31538946-31538996	AG10803	skin:	n/a
48	chr16:31538946-31538996	LNCaP	prostate:	n/a
49	chr16:31538946-31538996	Caco-2	colon:	n/a
50	chr16:31538946-31538996	PANC-1	pancreas:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31537316..31539067-chr16:31539316..31542062,2	K562	blood:
2	chr16:31493200..31498370-chr16:31536887..31540209,4	K562	blood:
3	chr16:31517756..31521127-chr16:31538452..31541350,5	K562	blood:
4	chr16:31517850..31520614-chr16:31538452..31541283,3	K562	blood:

No data

Variant related genes	Relation type
AHSP	TF binding region
AHSP	CpG island
ENSG00000140688	Chromatin interaction
ENSG00000260625	Chromatin interaction
ENSG00000140675	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11150627	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11866003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13338939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13339026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28496948	0.82[ASN][1000 genomes]
rs28509322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28788792	0.82[ASN][1000 genomes]
rs3813008	0.95[CEU][hapmap];1.00[MEX][hapmap]
rs4296276	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4411513	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs4503808	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4553646	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4564590	0.82[ASN][1000 genomes]
rs4889545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4889667	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4889670	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4889671	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4889672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56060924	0.90[EUR][1000 genomes]
rs57204609	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs58618301	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs58729087	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59813627	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60075107	0.92[EUR][1000 genomes]
rs61183892	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs62053184	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62053205	0.96[ASN][1000 genomes]
rs62053209	0.94[ASN][1000 genomes]
rs62053210	0.94[ASN][1000 genomes]
rs7196030	0.81[ASN][1000 genomes]
rs7196319	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7196393	0.82[ASN][1000 genomes]
rs7202020	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203199	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056084	0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.96[ASN][1000 genomes]
rs8057393	0.96[ASN][1000 genomes]
rs9921592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9921597	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923241	0.96[ASN][1000 genomes]
rs9923480	0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs9928760	0.82[ASN][1000 genomes]
rs9929779	0.84[ASN][1000 genomes]
rs9929825	0.96[ASN][1000 genomes]
rs9937077	0.96[ASN][1000 genomes]
rs9937367	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
2	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
3	nsv905748	chr16:31427678-31559220	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
4	nsv905749	chr16:31427678-31565597	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	96 gene(s)	inside rSNPs	diseases
5	nsv905750	chr16:31427678-31587662	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
6	nsv905752	chr16:31436932-31565597	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases
7	nsv905753	chr16:31436932-31587662	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
8	nsv905754	chr16:31451699-31565597	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
9	nsv1060240	chr16:31495873-31581450	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
10	esv1823209	chr16:31521276-31580272	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv3344221	chr16:31526786-31821640	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	esv3323903	chr16:31526802-31821640	Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
13	esv3504445	chr16:31526873-31821580	Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
14	esv3504446	chr16:31526873-31821580	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
15	esv3366795	chr16:31534951-31827424	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4499252	ZNF267	cis	cerebellum	SCAN
rs4499252	COX6A2	cis	parietal	SCAN
rs4499252	NUPR1	cis	cerebellum	SCAN
rs4499252	CD2BP2	cis	cerebellum	SCAN
rs4499252	ERAF	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31538800-31539000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
2	chr16:31538800-31539000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
3	chr16:31538800-31539200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
4	chr16:31538800-31539200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
5	chr16:31538800-31539200	Enhancers	H9 Cell Line	embryonic stem cell
6	chr16:31538800-31539200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
7	chr16:31538800-31539400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
8	chr16:31538800-31539600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr16:31538800-31540800	Flanking Active TSS	K562	blood

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