Variant report

Variant	rs892015
Chromosome Location	chr19:39684909-39684910
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr19:39684201-39685123	A549	lung:	n/a	n/a
2	SP1	chr19:39684288-39685106	A549	lung:	n/a	n/a
3	CREB1	chr19:39684356-39684966	A549	lung:	n/a	n/a
4	BCL3	chr19:39684339-39685037	A549	lung:	n/a	chr19:39684802-39684815
5	FOXA1	chr19:39684774-39685003	HepG2	liver:	n/a	n/a
6	SIN3AK20	chr19:39684478-39685041	A549	lung:	n/a	n/a
7	FOXA1	chr19:39684761-39685026	HepG2	liver:	n/a	n/a
8	EP300	chr19:39684268-39685123	A549	lung:	n/a	chr19:39684529-39684542
9	REST	chr19:39684333-39685034	A549	lung:	n/a	n/a
10	SIN3AK20	chr19:39684411-39685008	A549	lung:	n/a	n/a
11	FOXA2	chr19:39684731-39684967	HepG2	liver:	n/a	n/a
12	CEBPB	chr19:39684824-39684968	HepG2	liver:	n/a	n/a
13	ETS1	chr19:39684428-39685000	A549	lung:	n/a	n/a
14	NR3C1	chr19:39684337-39684946	A549	lung:	n/a	n/a
15	MAX	chr19:39684053-39685113	A549	lung:	n/a	n/a
16	NR3C1	chr19:39684265-39684994	A549	lung:	n/a	n/a
17	BCL3	chr19:39684408-39685102	A549	lung:	n/a	chr19:39684802-39684815
18	FOXA2	chr19:39684467-39685036	A549	lung:	n/a	n/a
19	TCF12	chr19:39684475-39685056	A549	lung:	n/a	n/a
20	EP300	chr19:39684259-39685048	A549	lung:	n/a	chr19:39684529-39684542
21	SP1	chr19:39684220-39685128	A549	lung:	n/a	n/a
22	FOXA2	chr19:39684355-39685172	A549	lung:	n/a	n/a
23	GATA3	chr19:39684340-39685125	A549	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:39677174..39681975-chr19:39683439..39687085,6	MCF-7	breast:
2	chr19:39683585..39686543-chr19:39818875..39821716,2	MCF-7	breast:
3	chr19:39666393..39669331-chr19:39683166..39685486,2	K562	blood:
4	chr19:39521369..39524252-chr19:39683910..39686549,2	MCF-7	breast:
5	chr19:39610539..39613482-chr19:39683239..39685361,3	MCF-7	breast:
6	chr19:39645920..39648679-chr19:39684558..39687537,2	MCF-7	breast:
7	chr19:39615742..39618240-chr19:39683167..39686406,3	MCF-7	breast:
8	chr19:39684528..39687372-chr19:39688107..39690948,3	MCF-7	breast:
9	chr19:39676778..39680967-chr19:39681960..39686095,4	K562	blood:

No data

Variant related genes	Relation type
NCCRP1	TF binding region
ENSG00000130669	Chromatin interaction
ENSG00000161243	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11083511	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083512	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083513	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11668945	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672471	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11672475	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11672479	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11672787	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12462614	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12609028	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12609203	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12610064	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12610093	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12610618	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12974074	0.87[CHB][hapmap]
rs12974792	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12976040	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1808652	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2013626	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2319154	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2319155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2319156	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2873914	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58016205	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58278424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7508321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8100659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8103222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8103224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8104935	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8106521	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs892016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv1796470	chr19:39679379-39714631	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs892015	ZNF229	cis	cerebellum	SCAN
rs892015	B9D2	cis	cerebellum	SCAN
rs892015	CCDC8	cis	parietal	SCAN
rs892015	ZNF229	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39657800-39687600	Weak transcription	Right Atrium	heart
2	chr19:39669200-39685800	Weak transcription	NHEK	skin
3	chr19:39678600-39687400	Weak transcription	Spleen	Spleen
4	chr19:39683800-39686600	Weak transcription	HMEC	breast
5	chr19:39684200-39685000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr19:39684200-39685800	Enhancers	Duodenum Mucosa	Duodenum
7	chr19:39684400-39685000	Flanking Active TSS	A549	lung
8	chr19:39684400-39685400	Enhancers	Fetal Intestine Large	intestine
9	chr19:39684400-39685400	Enhancers	Placenta	Placenta
10	chr19:39684400-39686000	Enhancers	Hela-S3	cervix
11	chr19:39684600-39685000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:39684600-39685000	Enhancers	HSMMtube	muscle
13	chr19:39684800-39685000	Enhancers	Pancreas	Pancrea
14	chr19:39684800-39685000	Enhancers	HepG2	liver
15	chr19:39684800-39685800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:39684800-39685800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr19:39684800-39685800	Weak transcription	Esophagus	oesophagus
18	chr19:39684800-39686000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:39684800-39686400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:39684800-39686600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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