Variant report

Variant	rs6509546
Chromosome Location	chr19:52018474-52018475
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr19:52018131-52018520	HepG2	liver:	n/a	n/a
2	CTCF	chr19:52018130-52018486	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr19:52018088-52018549	HepG2	liver:	n/a	n/a
4	MAX	chr19:52018157-52018482	K562	blood:	n/a	chr19:52018163-52018173
5	RAD21	chr19:52017955-52018689	SK-N-SH	brain:	n/a	n/a
6	SMC3	chr19:52017902-52018587	SK-N-SH	brain:	n/a	n/a
7	ZNF143	chr19:52018170-52018524	GM12878	blood:	n/a	n/a
8	CBX3	chr19:52018162-52018489	K562	blood:	n/a	n/a
9	RAD21	chr19:52018204-52018535	MCF-7	breast:	n/a	n/a
10	CTCF	chr19:52018193-52018477	GM12878	blood:	n/a	n/a
11	CTCF	chr19:52018114-52018624	HCT-116	colon:	n/a	n/a
12	CTCF	chr19:52018129-52018578	IMR90	lung:	n/a	n/a
13	RAD21	chr19:52018127-52018572	Hela-S3	cervix:	n/a	n/a
14	RAD21	chr19:52018122-52018516	HepG2	liver:	n/a	n/a
15	CTCF	chr19:52018201-52018474	SK-N-SH_RA	brain:	n/a	n/a
16	CTCF	chr19:52018031-52018612	MCF-7	breast:	n/a	n/a
17	RAD21	chr19:52018146-52018476	SK-N-SH_RA	brain:	n/a	n/a
18	CTCF	chr19:52018076-52018544	K562	blood:	n/a	n/a
19	CTCF	chr19:52018171-52018477	Spleen_OC	spleen:	n/a	n/a
20	CTCF	chr19:52017778-52018755	A549	lung:	n/a	n/a
21	SMC3	chr19:52018085-52018584	GM12878	blood:	n/a	n/a
22	CTCF	chr19:52018079-52018536	A549	lung:	n/a	n/a
23	CTCF	chr19:52018125-52018538	GM12878	blood:	n/a	n/a
24	CBX3	chr19:52018103-52018547	K562	blood:	n/a	n/a
25	RAD21	chr19:52018150-52018485	GM12878	blood:	n/a	n/a
26	RAD21	chr19:52018153-52018486	H1-hESC	embryonic stem cell:	n/a	n/a
27	NR2F2	chr19:52018134-52018507	K562	blood:	n/a	n/a
28	TEAD4	chr19:52018097-52018539	K562	blood:	n/a	n/a
29	CEBPB	chr19:52018138-52018490	K562	blood:	n/a	n/a
30	RUNX3	chr19:52018144-52018539	GM12878	blood:	n/a	n/a
31	SMC3	chr19:52018114-52018543	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr19:52018218-52018618	Lung_OC	lung:	n/a	n/a
33	CTCF	chr19:52018065-52018733	SK-N-SH	brain:	n/a	n/a
34	CTCF	chr19:52018257-52018522	ECC-1	luminal epithelium:	n/a	n/a
35	ZNF143	chr19:52018175-52018581	K562	blood:	n/a	n/a
36	REST	chr19:52018151-52018552	HL-60	blood:	n/a	n/a
37	EP300	chr19:52018166-52018583	K562	blood:	n/a	n/a
38	MYC	chr19:52018189-52018503	K562	blood:	n/a	n/a
39	RUNX3	chr19:52018123-52018480	GM12878	blood:	n/a	n/a
40	MAZ	chr19:52018076-52018510	K562	blood:	n/a	n/a
41	CTCF	chr19:52018209-52018507	HUVEC	blood vessel:	n/a	n/a
42	ARID3A	chr19:52018113-52018686	K562	blood:	n/a	n/a
43	IRF1	chr19:52018143-52018608	K562	blood:	n/a	n/a
44	CTCF	chr19:52018400-52018550	A549	lung:	n/a	n/a
45	JUND	chr19:52018104-52018527	K562	blood:	n/a	n/a
46	CTCF	chr19:52018380-52018530	HAc	cerebellar:	n/a	n/a
47	CEBPB	chr19:52018124-52018513	K562	blood:	n/a	n/a
48	CTCF	chr19:52018066-52018734	K562	blood:	n/a	n/a
49	ARID3A	chr19:52018198-52018479	HepG2	liver:	n/a	n/a
50	CTCF	chr19:52018170-52018509	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:51976116..51976755-chr19:52018185..52018795,2	MCF-7	breast:
2	chr19:52016872..52019391-chr19:52020928..52022569,2	K562	blood:
3	chr19:52017645..52019212-chr19:52145235..52147486,2	MCF-7	breast:
4	chr19:52016307..52018476-chr19:52032944..52035173,2	K562	blood:
5	chr19:51975937..51976795-chr19:52018276..52018797,2	MCF-7	breast:
6	chr19:52017775..52020070-chr19:52020928..52023359,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268777	TF binding region
ENSG00000105492	Chromatin interaction
ENSG00000268777	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10221508	0.93[ASN][1000 genomes]
rs12461985	0.89[ASN][1000 genomes]
rs12609761	0.89[JPT][hapmap]
rs7246846	0.82[GIH][hapmap]
rs8105348	0.89[JPT][hapmap]
rs8106176	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8106598	0.82[LWK][hapmap]
rs9807820	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6509546	CHMP2A	cis	parietal	SCAN
rs6509546	NAT14	cis	cerebellum	SCAN
rs6509546	NLRP5	cis	cerebellum	SCAN
rs6509546	SIGLEC12	cis	Whole Blood	GTEx
rs6509546	IL11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52017400-52018800	Enhancers	K562	blood
2	chr19:52018000-52018600	Enhancers	Primary B cells from peripheral blood	blood
3	chr19:52018400-52021400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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