Variant report

Variant	rs11665924
Chromosome Location	chr19:44286982-44286983
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:68)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:68 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr19:44286401-44287324	K562	blood:	n/a	n/a
2	FOS	chr19:44286846-44287317	MCF10A-Er-Src	breast:	n/a	n/a
3	E2F1	chr19:44286935-44287462	Hela-S3	cervix:	n/a	chr19:44287253-44287264 chr19:44287324-44287334
4	JUND	chr19:44286524-44287147	K562	blood:	n/a	n/a
5	NR2C2	chr19:44285391-44287077	GM12878	blood:	n/a	n/a
6	MYC	chr19:44286865-44287101	Hela-S3	cervix:	n/a	n/a
7	RELA	chr19:44286496-44287320	GM19193	blood:	n/a	n/a
8	TCF3	chr19:44286898-44287428	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:44286719-44287169	GM12878	blood:	n/a	n/a
10	FOS	chr19:44286851-44287189	MCF10A-Er-Src	breast:	n/a	n/a
11	MAX	chr19:44286401-44287086	K562	blood:	n/a	n/a
12	RUNX3	chr19:44286289-44287308	GM12878	blood:	n/a	n/a
13	EP300	chr19:44286447-44287285	K562	blood:	n/a	n/a
14	RCOR1	chr19:44286456-44287483	Hela-S3	cervix:	n/a	n/a
15	CHD2	chr19:44286476-44287511	Hela-S3	cervix:	n/a	n/a
16	BRCA1	chr19:44286814-44287466	Hela-S3	cervix:	n/a	n/a
17	MXI1	chr19:44286761-44287479	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr19:44286915-44287020	GM19239	blood:	n/a	n/a
19	TBP	chr19:44286495-44287301	K562	blood:	n/a	n/a
20	MAX	chr19:44286439-44287482	Hela-S3	cervix:	n/a	n/a
21	TFAP2A	chr19:44286655-44287484	Hela-S3	cervix:	n/a	n/a
22	E2F6	chr19:44286424-44287446	Hela-S3	cervix:	n/a	chr19:44287324-44287334 chr19:44287254-44287265
23	RCOR1	chr19:44286232-44287133	K562	blood:	n/a	n/a
24	FOS	chr19:44286808-44287301	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr19:44286743-44287031	Hela-S3	cervix:	n/a	n/a
26	E2F6	chr19:44286536-44287464	K562	blood:	n/a	chr19:44287324-44287334 chr19:44287254-44287265
27	POLR2A	chr19:44286734-44287561	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr19:44286921-44287016	MCF-7	breast:	n/a	n/a
29	MAZ	chr19:44286678-44287487	Hela-S3	cervix:	n/a	n/a
30	RUNX3	chr19:44286278-44287303	GM12878	blood:	n/a	n/a
31	ELF1	chr19:44286509-44287322	GM12878	blood:	n/a	n/a
32	FOS	chr19:44286803-44287345	MCF10A-Er-Src	breast:	n/a	n/a
33	STAT3	chr19:44286863-44287372	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr19:44286711-44287018	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr19:44286597-44287543	Hela-S3	cervix:	n/a	n/a
36	MAX	chr19:44284653-44287580	A549	lung:	n/a	n/a
37	POLR2A	chr19:44286275-44287458	GM12892	blood:	n/a	n/a
38	MYC	chr19:44286883-44287072	MCF-7	breast:	n/a	n/a
39	TFAP2C	chr19:44285948-44287558	Hela-S3	cervix:	n/a	n/a
40	MTA3	chr19:44284663-44287383	GM12878	blood:	n/a	n/a
41	HMGN3	chr19:44286946-44287435	K562	blood:	n/a	n/a
42	POLR2A	chr19:44286485-44287478	GM18505	blood:	n/a	n/a
43	E2F6	chr19:44286814-44287009	K562	blood:	n/a	n/a
44	MAX	chr19:44284808-44287558	HCT-116	colon:	n/a	n/a
45	TEAD4	chr19:44286330-44287034	K562	blood:	n/a	chr19:44286797-44286806
46	MYC	chr19:44286752-44287417	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr19:44286434-44287603	GM12892	blood:	n/a	n/a
48	TCF7L2	chr19:44286603-44287481	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr19:44286823-44287501	Hela-S3	cervix:	n/a	n/a
50	MAX	chr19:44285845-44287442	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:44254856..44260610-chr19:44285479..44289743,8	MCF-7	breast:
2	chr19:44285151..44287673-chr19:44304698..44307522,2	K562	blood:
3	chr19:44248016..44250169-chr19:44285540..44287422,2	MCF-7	breast:
4	chr19:44256760..44265122-chr19:44281375..44290996,18	K562	blood:
5	chr19:44256245..44259869-chr19:44284477..44291035,7	MCF-7	breast:
6	chr19:44252620..44255396-chr19:44285758..44288205,2	MCF-7	breast:

No data

Variant related genes	Relation type
KCNN4	TF binding region
ENSG00000159871	Chromatin interaction
ENSG00000105771	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10404672	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10404692	0.82[AMR][1000 genomes]
rs10405457	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10421887	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10422990	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11669175	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11670158	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11671215	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12460161	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12463370	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12974061	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs349045	0.83[CHB][hapmap]
rs349046	0.92[CHB][hapmap];0.90[CHD][hapmap]
rs349047	0.92[CHB][hapmap];0.90[CHD][hapmap]
rs349049	0.92[CHB][hapmap];0.90[CHD][hapmap]
rs349050	0.91[CHB][hapmap]
rs3760982	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3760983	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3760984	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4802199	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4802200	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803658	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60184524	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61138927	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11665924	GEMIN7	cis	cerebellum	SCAN
rs11665924	KCNN4	cis	Whole Blood	GTEx
rs11665924	AC115522.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11665924	KDELR1	cis	parietal	SCAN
rs11665924	ZNF404	trans	parietal	SCAN
rs11665924	ZNF296	cis	parietal	SCAN
rs11665924	ZNF296	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44281400-44287000	Enhancers	Spleen	Spleen
2	chr19:44282400-44289200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:44284000-44288600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:44284200-44287800	Weak transcription	Dnd41	blood
5	chr19:44284400-44287600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:44284400-44288400	Weak transcription	HUVEC	blood vessel
7	chr19:44285000-44287000	Enhancers	NHDF-Ad	bronchial
8	chr19:44285000-44287400	Flanking Active TSS	Primary B cells from peripheral blood	blood
9	chr19:44285200-44287000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:44285200-44287400	Flanking Active TSS	GM12878-XiMat	blood
11	chr19:44285200-44289400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr19:44285200-44289400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr19:44285200-44289600	Enhancers	Esophagus	oesophagus
14	chr19:44285400-44287000	Enhancers	Primary T cells from cord blood	blood
15	chr19:44285400-44287000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:44285400-44287000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:44285400-44287200	Flanking Active TSS	Hela-S3	cervix
18	chr19:44285400-44287400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr19:44285400-44288600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:44285400-44288800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:44285400-44291400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:44285600-44287000	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr19:44285600-44288000	Weak transcription	Primary B cells from cord blood	blood
24	chr19:44285600-44288000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr19:44285600-44288600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr19:44285800-44287000	Enhancers	Placenta	Placenta
27	chr19:44285800-44287000	Enhancers	HMEC	breast
28	chr19:44285800-44287600	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr19:44285800-44288000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr19:44285800-44288000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr19:44285800-44288200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr19:44285800-44288200	Enhancers	NHEK	skin
33	chr19:44285800-44288400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:44285800-44288400	Weak transcription	HSMMtube	muscle
35	chr19:44285800-44288600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr19:44285800-44288600	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr19:44285800-44289200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr19:44285800-44289400	Enhancers	Stomach Mucosa	stomach
39	chr19:44285800-44289800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:44286000-44287000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr19:44286000-44287200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:44286000-44287800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr19:44286000-44288000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr19:44286000-44288000	Weak transcription	NHLF	lung
45	chr19:44286000-44288200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:44286000-44288200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:44286000-44288200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr19:44286000-44288200	Weak transcription	HSMM	muscle
49	chr19:44286000-44288200	Weak transcription	NH-A	brain
50	chr19:44286000-44288200	Weak transcription	Osteobl	bone

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