Variant report

Variant	rs11878620
Chromosome Location	chr19:42747229-42747230
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	POLR2A	chr19:42746381-42747824	MCF-7	breast:	n/a	n/a
2	MAX	chr19:42746646-42747717	Hela-S3	cervix:	n/a	chr19:42746833-42746842
3	USF1	chr19:42746734-42747652	H1-hESC	embryonic stem cell:	n/a	chr19:42746749-42746765 chr19:42746751-42746767
4	IRF1	chr19:42746618-42747814	K562	blood:	n/a	n/a
5	RELA	chr19:42746578-42747879	GM10847	blood:	n/a	n/a
6	GABPA	chr19:42746608-42747659	HL-60	blood:	n/a	n/a
7	ELK1	chr19:42746764-42747667	K562	blood:	n/a	n/a
8	POLR2A	chr19:42745973-42747912	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr19:42746170-42749635	K562	blood:	n/a	n/a
10	YY1	chr19:42746673-42747820	H1-hESC	embryonic stem cell:	n/a	chr19:42746749-42746763 chr19:42746797-42746806
11	BCL3	chr19:42746581-42748056	A549	lung:	n/a	chr19:42746633-42746646 chr19:42746751-42746764 chr19:42746755-42746768
12	CREB1	chr19:42746484-42747776	HepG2	liver:	n/a	n/a
13	REST	chr19:42746468-42747771	H1-neurons	neurons:	n/a	chr19:42746799-42746812
14	SMC3	chr19:42746840-42747585	GM12878	blood:	n/a	n/a
15	BCLAF1	chr19:42746386-42747804	GM12878	blood:	n/a	chr19:42746633-42746646 chr19:42746751-42746764 chr19:42746755-42746768
16	CTCF	chr19:42746342-42749547	SK-N-SH	brain:	n/a	n/a
17	GABPA	chr19:42746651-42747936	A549	lung:	n/a	n/a
18	NFYB	chr19:42746860-42747537	Hela-S3	cervix:	n/a	n/a
19	RCOR1	chr19:42746724-42747624	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:42747111-42747599	H1-hESC	embryonic stem cell:	n/a	n/a
21	ETS1	chr19:42746569-42747976	A549	lung:	n/a	chr19:42746924-42746937 chr19:42746774-42746787 chr19:42746848-42746861
22	EBF1	chr19:42747047-42747369	GM12878	blood:	n/a	n/a
23	CREB1	chr19:42746563-42747673	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr19:42746351-42748014	ECC-1	luminal epithelium:	n/a	n/a
25	YY1	chr19:42746592-42747755	H1-hESC	embryonic stem cell:	n/a	chr19:42746749-42746763 chr19:42746797-42746806
26	SPI1	chr19:42747152-42747422	K562	blood:	n/a	n/a
27	FOXA2	chr19:42747044-42747701	A549	lung:	n/a	n/a
28	MTA3	chr19:42746693-42747987	GM12878	blood:	n/a	n/a
29	YY1	chr19:42746686-42747738	HepG2	liver:	n/a	chr19:42746749-42746763 chr19:42746797-42746806
30	MYC	chr19:42746722-42747743	K562	blood:	n/a	chr19:42746833-42746842
31	TAF1	chr19:42747170-42747797	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr19:42746203-42747927	Hela-S3	cervix:	n/a	n/a
33	SIN3AK20	chr19:42747032-42747647	PANC-1	pancreas:	n/a	n/a
34	POLR2A	chr19:42746412-42747781	PANC-1	pancreas:	n/a	n/a
35	SRF	chr19:42746589-42747691	ECC-1	luminal epithelium:	n/a	n/a
36	ELK1	chr19:42746742-42747535	GM12878	blood:	n/a	n/a
37	ZEB1	chr19:42746498-42747901	HepG2	liver:	n/a	n/a
38	JUND	chr19:42746735-42747465	HepG2	liver:	n/a	n/a
39	YY1	chr19:42746615-42747802	SK-N-SH	brain:	n/a	chr19:42746749-42746763 chr19:42746797-42746806
40	E2F4	chr19:42746635-42747652	K562	blood:	n/a	chr19:42746880-42746891 chr19:42746797-42746806 chr19:42746893-42746904
41	STAT3	chr19:42746864-42747775	MCF10A-Er-Src	breast:	n/a	chr19:42747373-42747384
42	POLR2A	chr19:42746356-42747982	H1-hESC	embryonic stem cell:	n/a	n/a
43	UBTF	chr19:42746040-42747834	K562	blood:	n/a	n/a
44	STAT5A	chr19:42746680-42747739	K562	blood:	n/a	n/a
45	ATF2	chr19:42746636-42747667	GM12878	blood:	n/a	n/a
46	STAT3	chr19:42746922-42747734	Hela-S3	cervix:	n/a	chr19:42747373-42747384
47	RELA	chr19:42746653-42747589	GM19193	blood:	n/a	n/a
48	TEAD4	chr19:42746666-42747889	K562	blood:	n/a	n/a
49	TRIM28	chr19:42746643-42747926	K562	blood:	n/a	n/a
50	GABPA	chr19:42746563-42747603	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42719158..42725942-chr19:42744280..42751391,14	MCF-7	breast:
2	chr19:42722142..42727268-chr19:42743805..42748670,12	MCF-7	breast:
3	chr19:42746881..42748655-chr19:42811057..42812701,2	K562	blood:
4	chr19:42746221..42749028-chr19:42806673..42809269,4	K562	blood:
5	chr19:42745106..42750336-chr19:42827948..42831181,5	K562	blood:
6	chr19:42634611..42641780-chr19:42741001..42747645,8	MCF-7	breast:
7	chr19:42747132..42763787-chr19:42768368..42776785,67	MCF-7	breast:
8	chr19:42747157..42748749-chr19:42804918..42806482,2	K562	blood:
9	chr19:42747088..42748068-chr19:42783977..42784681,2	Hela-S3	cervix:
10	chr19:42745670..42748955-chr19:42805967..42808847,6	K562	blood:
11	chr19:42432401..42434702-chr19:42746982..42749095,2	K562	blood:
12	chr19:42619346..42621676-chr19:42746420..42748226,2	MCF-7	breast:
13	chr19:42745110..42750037-chr19:42804255..42809210,7	MCF-7	breast:
14	chr19:42626781..42629013-chr19:42746028..42748919,2	K562	blood:
15	chr19:42744297..42761073-chr19:42776978..42802286,113	MCF-7	breast:
16	chr19:42746379..42748753-chr19:42901046..42902799,2	K562	blood:
17	chr19:42720291..42721967-chr19:42744668..42747834,3	MCF-7	breast:
18	chr19:42734779..42737067-chr19:42745327..42747787,2	MCF-7	breast:
19	chr19:42747027..42748730-chr19:42805186..42807872,2	MCF-7	breast:
20	chr19:42745751..42747885-chr19:42828050..42829792,2	MCF-7	breast:
21	chr19:42362466..42365153-chr19:42745908..42747542,2	K562	blood:
22	chr19:42747001..42747936-chr7:44122025..44122598,2	Hela-S3	cervix:
23	chr19:42633522..42638694-chr19:42746138..42750554,7	MCF-7	breast:
24	chr19:42743599..42762610-chr19:42780302..42801550,102	MCF-7	breast:

Variant related genes	Relation type
GSK3A	TF binding region
ENSG00000028277	Chromatin interaction
ENSG00000213904	Chromatin interaction
ENSG00000079432	Chromatin interaction
ENSG00000105372	Chromatin interaction
ENSG00000160570	Chromatin interaction
ENSG00000266226	Chromatin interaction
ENSG00000079462	Chromatin interaction
ENSG00000167625	Chromatin interaction
ENSG00000188368	Chromatin interaction
ENSG00000254887	Chromatin interaction
ENSG00000122678	Chromatin interaction
ENSG00000076928	Chromatin interaction
ENSG00000105429	Chromatin interaction
ENSG00000105723	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10407506	0.80[LWK][hapmap];0.83[YRI][hapmap]
rs10410185	0.82[CHB][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs10410198	0.82[CHB][hapmap];0.91[ASN][1000 genomes]
rs10410698	0.82[CHB][hapmap];0.91[ASN][1000 genomes]
rs10412833	0.82[ASN][1000 genomes]
rs10426306	0.91[ASN][1000 genomes]
rs10426310	0.91[ASN][1000 genomes]
rs10500285	0.86[GIH][hapmap]
rs11557114	0.91[ASN][1000 genomes]
rs11880124	0.86[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11882654	0.91[ASN][1000 genomes]
rs11883412	0.81[ASW][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs1206009	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs1206027	0.82[CHB][hapmap]
rs1206029	0.82[CHB][hapmap];0.80[MEX][hapmap]
rs1206033	0.82[CHB][hapmap]
rs1206038	0.82[CHB][hapmap]
rs1206040	0.82[CHB][hapmap]
rs1206041	0.82[CHB][hapmap]
rs1206044	0.82[CHB][hapmap]
rs1209280	0.82[ASN][1000 genomes]
rs1211265	0.82[ASN][1000 genomes]
rs1613100	0.82[CHB][hapmap]
rs1654623	0.82[CHB][hapmap]
rs1676211	0.82[CHB][hapmap]
rs1676217	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs1676221	0.82[CHB][hapmap]
rs1676222	0.82[CHB][hapmap]
rs1685565	0.82[CHB][hapmap]
rs16975663	0.94[LWK][hapmap];1.00[YRI][hapmap]
rs16975684	0.93[GIH][hapmap];0.80[MEX][hapmap]
rs17270169	0.86[GIH][hapmap]
rs2267630	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs2302485	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2303652	0.81[ASW][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2537697	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs2615614	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs28537976	0.91[ASN][1000 genomes]
rs28621009	0.82[CHB][hapmap]
rs35493131	0.91[ASN][1000 genomes]
rs3745231	0.93[GIH][hapmap];0.91[MEX][hapmap]
rs3745233	0.81[ASW][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes]
rs3810148	0.82[CHB][hapmap];0.80[MEX][hapmap];0.87[ASN][1000 genomes]
rs3826705	0.86[GIH][hapmap]
rs4141062	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs57938324	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7248379	0.93[GIH][hapmap];0.80[MEX][hapmap]
rs7258795	0.91[ASN][1000 genomes]
rs73552881	0.91[ASN][1000 genomes]
rs73552895	0.91[ASN][1000 genomes]
rs741070	0.82[CHB][hapmap];0.91[ASN][1000 genomes]
rs8182491	0.93[GIH][hapmap];0.80[MEX][hapmap]
rs851296	0.82[CHB][hapmap]
rs851612	0.87[ASN][1000 genomes]
rs851615	0.82[ASN][1000 genomes]
rs9636121	0.82[CHB][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats 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
5	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
7	nsv833833	chr19:42657276-42783122	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
9	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
10	nsv833834	chr19:42736444-42835027	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	42 gene(s)	inside rSNPs	diseases
11	nsv911784	chr19:42741124-42787664	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
12	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
13	nsv911786	chr19:42744234-42797959	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	39 gene(s)	inside rSNPs	diseases
14	esv3352699	chr19:42745662-42747910	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42744600-42748800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:42745000-42748000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:42745200-42748200	Active TSS	HSMM	muscle
4	chr19:42745400-42748400	Active TSS	H1 Cell Line	embryonic stem cell
5	chr19:42745400-42749200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:42745600-42748200	Active TSS	Right Atrium	heart
7	chr19:42745600-42748800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr19:42745600-42749000	Active TSS	Right Ventricle	heart
9	chr19:42745600-42749200	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr19:42745800-42747600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:42745800-42748200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:42745800-42748200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr19:42745800-42748800	Active TSS	Gastric	stomach
14	chr19:42745800-42749000	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr19:42745800-42749000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:42745800-42749000	Active TSS	Aorta	Aorta
17	chr19:42745800-42749000	Active TSS	Lung	lung
18	chr19:42745800-42749000	Active TSS	Ovary	ovary
19	chr19:42745800-42749200	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr19:42745800-42749200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr19:42745800-42749200	Active TSS	Esophagus	oesophagus
22	chr19:42745800-42749200	Active TSS	Left Ventricle	heart
23	chr19:42745800-42749200	Active TSS	Stomach Mucosa	stomach
24	chr19:42745800-42749200	Active TSS	NHDF-Ad	bronchial
25	chr19:42746000-42747400	Active TSS	Fetal Thymus	thymus
26	chr19:42746000-42747600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:42746000-42747600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:42746000-42747600	Active TSS	Brain Germinal Matrix	brain
29	chr19:42746000-42747600	Active TSS	Thymus	Thymus
30	chr19:42746000-42747600	Active TSS	NH-A	brain
31	chr19:42746000-42747800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr19:42746000-42747800	Active TSS	Muscle Satellite Cultured Cells	--
33	chr19:42746000-42747800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:42746000-42747800	Active TSS	Placenta	Placenta
35	chr19:42746000-42747800	Bivalent/Poised TSS	HepG2	liver
36	chr19:42746000-42748200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:42746000-42748200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:42746000-42748200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:42746000-42748200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:42746000-42748200	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr19:42746000-42748200	Active TSS	Placenta Amnion	Placenta Amnion
42	chr19:42746000-42748200	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr19:42746000-42748200	Active TSS	HMEC	breast
44	chr19:42746000-42748200	Active TSS	Osteobl	bone
45	chr19:42746000-42748600	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr19:42746000-42748600	Active TSS	NHLF	lung
47	chr19:42746000-42749000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr19:42746000-42749000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr19:42746000-42749000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr19:42746000-42749000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links