Variant report

Variant	rs11880579
Chromosome Location	chr19:42348717-42348718
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	MAX	chr19:42348611-42349053	ECC-1	luminal epithelium:	n/a	chr19:42348672-42348681
3	E2F6	chr19:42348642-42349134	H1-hESC	embryonic stem cell:	n/a	chr19:42348759-42348769 chr19:42348783-42348792 chr19:42348787-42348797
4	MAX	chr19:42348633-42349150	H1-hESC	embryonic stem cell:	n/a	chr19:42348672-42348681
5	CBX3	chr19:42348710-42349230	K562	blood:	n/a	n/a
6	MAX	chr19:42348632-42348987	ECC-1	luminal epithelium:	n/a	chr19:42348672-42348681
7	E2F6	chr19:42348639-42349154	K562	blood:	n/a	chr19:42348759-42348769 chr19:42348783-42348792 chr19:42348787-42348797
8	E2F6	chr19:42348647-42349128	A549	lung:	n/a	chr19:42348759-42348769 chr19:42348783-42348792 chr19:42348787-42348797
9	E2F6	chr19:42348561-42349267	A549	lung:	n/a	chr19:42348759-42348769 chr19:42348783-42348792 chr19:42348787-42348797
10	E2F6	chr19:42348622-42348956	K562	blood:	n/a	chr19:42348759-42348769 chr19:42348783-42348792 chr19:42348787-42348797
11	MAX	chr19:42348623-42349074	K562	blood:	n/a	chr19:42348672-42348681
12	E2F6	chr19:42348673-42348946	K562	blood:	n/a	chr19:42348759-42348769 chr19:42348783-42348792 chr19:42348787-42348797
13	MAX	chr19:42348527-42349191	A549	lung:	n/a	chr19:42348672-42348681

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:42348686-42348736	HCT-116	colon:	n/a
2	chr19:42348676-42348726	PrEC	prostate:	n/a
3	chr19:42348676-42348726	HPAEpiC	pulmonary alveolar:	n/a
4	chr19:42348686-42348736	HRE	kidney:	n/a
5	chr19:42348676-42348726	PFSK-1	brain:	n/a
6	chr19:42348686-42348736	CMK	blood:	n/a
7	chr19:42348686-42348736	SAEC	small airway:	n/a
8	chr19:42348676-42348726	RPTEC	kidney:	n/a
9	chr19:42348686-42348736	AG09319	gingival:	n/a
10	chr19:42348686-42348736	GM12892	blood:	n/a
11	chr19:42348676-42348726	T-47D	breast:	n/a
12	chr19:42348686-42348736	GM12878	blood:	n/a
13	chr19:42348686-42348736	AG04449	skin:	fetal
14	chr19:42348686-42348736	PrEC	prostate:	n/a
15	chr19:42348676-42348726	HCT-116	colon:	n/a
16	chr19:42348676-42348726	HNPCEpiC	eye:	n/a
17	chr19:42348676-42348726	HMEC	breast:	n/a
18	chr19:42348686-42348736	HCM	heart:	n/a
19	chr19:42348676-42348726	NHDF-neo	bronchial:	n/a
20	chr19:42348686-42348736	HNPCEpiC	eye:	n/a
21	chr19:42348686-42348736	SK-N-SH_RA	brain:	n/a
22	chr19:42348686-42348736	HCF	heart:	n/a
23	chr19:42348676-42348726	CMK	blood:	n/a
24	chr19:42348686-42348736	MCF-7	breast:	n/a
25	chr19:42348676-42348726	SK-N-SH_RA	brain:	n/a
26	chr19:42348676-42348726	GM06990	blood:	n/a
27	chr19:42348676-42348726	SK-N-SH	brain:	n/a
28	chr19:42348686-42348736	ProgFib	skin:	n/a
29	chr19:42348676-42348726	AG10803	skin:	n/a
30	chr19:42348676-42348726	K562	blood:	n/a
31	chr19:42348676-42348726	HEEpiC	esophagus:	n/a
32	chr19:42348676-42348726	HIPEpiC	eye:	n/a
33	chr19:42348676-42348726	HRPEpiC	eye:	n/a
34	chr19:42348686-42348736	AG04450	lung:	fetal
35	chr19:42348676-42348726	NH-A	brain:	n/a
36	chr19:42348676-42348726	NT2-D1	testis:	n/a
37	chr19:42348676-42348726	BJ	skin:	n/a
38	chr19:42348686-42348736	LNCaP	prostate:	n/a
39	chr19:42348686-42348736	HRPEpiC	eye:	n/a
40	chr19:42348686-42348736	NT2-D1	testis:	n/a
41	chr19:42348676-42348726	HUVEC	blood vessel:	n/a
42	chr19:42348686-42348736	U87	brain:	n/a
43	chr19:42348676-42348726	Hela-S3	cervix:	n/a
44	chr19:42348676-42348726	AG09319	gingival:	n/a
45	chr19:42348676-42348726	U87	brain:	n/a
46	chr19:42348686-42348736	HEK293	kidney:	embryo
47	chr19:42348686-42348736	HIPEpiC	eye:	n/a
48	chr19:42348686-42348736	IMR90	lung:	fetal
49	chr19:42348686-42348736	NHDF-neo	bronchial:	n/a
50	chr19:42348676-42348726	ovcar-3	ovarian:	n/a

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:

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

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11083640	0.80[YRI][hapmap];1.00[AMR][1000 genomes]
rs11878330	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11878687	1.00[ASW][hapmap];1.00[EUR][1000 genomes]
rs11879132	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11879519	1.00[EUR][1000 genomes]
rs11879631	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11880116	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11880522	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11881323	0.80[YRI][hapmap]
rs11881984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12327868	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3745223	0.80[YRI][hapmap]
rs61761235	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73932094	1.00[EUR][1000 genomes]
rs8103772	1.00[EUR][1000 genomes]
rs8112569	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:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42348000-42349200	Enhancers	K562	blood
2	chr19:42348400-42349000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:42348600-42349000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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