Variant report

Variant	rs11878687
Chromosome Location	chr19:42349054-42349055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:122)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr19:42348531-42349191	H1-hESC	embryonic stem cell:	n/a	chr19:42348759-42348769 chr19:42348783-42348792 chr19:42348787-42348797
2	E2F6	chr19:42348642-42349134	H1-hESC	embryonic stem cell:	n/a	chr19:42348759-42348769 chr19:42348783-42348792 chr19:42348787-42348797
3	NFYB	chr19:42348761-42349134	K562	blood:	n/a	n/a
4	GABPA	chr19:42348735-42349186	K562	blood:	n/a	chr19:42348783-42348792
5	NFYA	chr19:42348829-42349160	K562	blood:	n/a	n/a
6	MAX	chr19:42348633-42349150	H1-hESC	embryonic stem cell:	n/a	chr19:42348672-42348681
7	CBX3	chr19:42348710-42349230	K562	blood:	n/a	n/a
8	E2F6	chr19:42348639-42349154	K562	blood:	n/a	chr19:42348759-42348769 chr19:42348783-42348792 chr19:42348787-42348797
9	MAX	chr19:42348718-42349103	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr19:42348647-42349128	A549	lung:	n/a	chr19:42348759-42348769 chr19:42348783-42348792 chr19:42348787-42348797
11	E2F6	chr19:42348561-42349267	A549	lung:	n/a	chr19:42348759-42348769 chr19:42348783-42348792 chr19:42348787-42348797
12	MAX	chr19:42348623-42349074	K562	blood:	n/a	chr19:42348672-42348681
13	MAX	chr19:42348527-42349191	A549	lung:	n/a	chr19:42348672-42348681
14	CBX3	chr19:42348834-42349176	K562	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:42349032-42349082	PANC-1	pancreas:	n/a
2	chr19:42349010-42349060	AG10803	skin:	n/a
3	chr19:42349010-42349060	HCT-116	colon:	n/a
4	chr19:42349010-42349060	HRCEpiC	kidney:	n/a
5	chr19:42349010-42349060	HMEC	breast:	n/a
6	chr19:42349010-42349060	HepG2	liver:	n/a
7	chr19:42349010-42349060	HRE	kidney:	n/a
8	chr19:42349010-42349060	PFSK-1	brain:	n/a
9	chr19:42349032-42349082	H1-hESC	embryonic stem cell:	embryo
10	chr19:42349010-42349060	LNCaP	prostate:	n/a
11	chr19:42349032-42349082	Hepatocyte	liver:	n/a
12	chr19:42349010-42349060	NT2-D1	testis:	n/a
13	chr19:42349010-42349060	SAEC	small airway:	n/a
14	chr19:42349010-42349060	HEEpiC	esophagus:	n/a
15	chr19:42349032-42349082	SAEC	small airway:	n/a
16	chr19:42349010-42349060	T-47D	breast:	n/a
17	chr19:42349032-42349082	HEK293	kidney:	embryo
18	chr19:42349032-42349082	AG10803	skin:	n/a
19	chr19:42349032-42349082	HCF	heart:	n/a
20	chr19:42349032-42349082	GM19239	blood:	n/a
21	chr19:42349010-42349060	HIPEpiC	eye:	n/a
22	chr19:42349010-42349060	Jurkat	blood:	n/a
23	chr19:42349010-42349060	A549	lung:	n/a
24	chr19:42349010-42349060	BJ	skin:	n/a
25	chr19:42349010-42349060	Hela-S3	cervix:	n/a
26	chr19:42349032-42349082	SK-N-SH	brain:	n/a
27	chr19:42349032-42349082	AG09309	skin:	n/a
28	chr19:42349032-42349082	MCF-7	breast:	n/a
29	chr19:42349032-42349082	HepG2	liver:	n/a
30	chr19:42349032-42349082	A549	lung:	n/a
31	chr19:42349032-42349082	AG04449	skin:	fetal
32	chr19:42349010-42349060	PrEC	prostate:	n/a
33	chr19:42349010-42349060	HNPCEpiC	eye:	n/a
34	chr19:42349032-42349082	HRE	kidney:	n/a
35	chr19:42349010-42349060	HEK293	kidney:	embryo
36	chr19:42349032-42349082	HAEpiC	amniotic membrane:	n/a
37	chr19:42349010-42349060	NHBE	bronchial:	n/a
38	chr19:42349010-42349060	NB4	blood:	n/a
39	chr19:42349032-42349082	HCPEpiC	choroid plexus:	n/a
40	chr19:42349010-42349060	AG09309	skin:	n/a
41	chr19:42349032-42349082	RPTEC	kidney:	n/a
42	chr19:42349032-42349082	HNPCEpiC	eye:	n/a
43	chr19:42349032-42349082	U87	brain:	n/a
44	chr19:42349010-42349060	NH-A	brain:	n/a
45	chr19:42349010-42349060	AG04450	lung:	fetal
46	chr19:42349032-42349082	HPAEpiC	pulmonary alveolar:	n/a
47	chr19:42349032-42349082	K562	blood:	n/a
48	chr19:42349032-42349082	CMK	blood:	n/a
49	chr19:42349010-42349060	SK-N-SH_RA	brain:	n/a
50	chr19:42349032-42349082	SK-N-MC	brain:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr19:42348714..42350614-chr19:42362981..42365600,2	MCF-7	breast:
2	chr19:42340672..42344473-chr19:42346449..42349067,4	K562	blood:
3	chr19:42346423..42349202-chr19:42351468..42355829,7	K562	blood:
4	chr19:42346706..42349091-chr19:42352503..42356782,5	K562	blood:
5	chr19:42347384..42349576-chr19:42363024..42365083,2	K562	blood:
6	chr19:42347384..42349429-chr19:42363024..42365795,2	K562	blood:

No data

Variant related genes	Relation type
DMRTC2	TF binding region
LYPD4	TF binding region
LYPD4	CpG island
DMRTC2	CpG island
ENSG00000183103	Chromatin interaction
ENSG00000142025	Chromatin interaction
ENSG00000105372	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11878330	1.00[EUR][1000 genomes]
rs11879437	1.00[MEX][hapmap];1.00[YRI][hapmap]
rs11879519	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11879631	1.00[EUR][1000 genomes]
rs11880522	1.00[EUR][1000 genomes]
rs11880579	1.00[ASW][hapmap];1.00[EUR][1000 genomes]
rs11880977	1.00[MEX][hapmap];0.82[YRI][hapmap]
rs11881323	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs11881932	1.00[AMR][1000 genomes]
rs11881984	1.00[EUR][1000 genomes]
rs11883018	0.90[YRI][hapmap]
rs12327868	1.00[EUR][1000 genomes]
rs34537433	1.00[MEX][hapmap]
rs41301951	1.00[AMR][1000 genomes]
rs7255488	1.00[MEX][hapmap]
rs73932094	1.00[EUR][1000 genomes]
rs8103772	1.00[EUR][1000 genomes]
rs8112569	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42348000-42349200	Enhancers	K562	blood

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