Variant report

Variant	rs3760982
Chromosome Location	chr19:44286513-44286514
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	MYC	chr19:44286401-44287324	K562	blood:	n/a	n/a
2	RCOR1	chr19:44286352-44286809	K562	blood:	n/a	n/a
3	NR2C2	chr19:44285391-44287077	GM12878	blood:	n/a	n/a
4	TBL1XR1	chr19:44286089-44286686	K562	blood:	n/a	n/a
5	RELA	chr19:44286496-44287320	GM19193	blood:	n/a	n/a
6	MAX	chr19:44286401-44287086	K562	blood:	n/a	n/a
7	RUNX3	chr19:44286289-44287308	GM12878	blood:	n/a	n/a
8	EGR1	chr19:44286461-44286677	K562	blood:	n/a	chr19:44286551-44286575 chr19:44286613-44286627 chr19:44286617-44286628
9	EP300	chr19:44286447-44287285	K562	blood:	n/a	n/a
10	UBTF	chr19:44286494-44286658	K562	blood:	n/a	n/a
11	RCOR1	chr19:44286456-44287483	Hela-S3	cervix:	n/a	n/a
12	FOS	chr19:44286365-44286522	MCF10A-Er-Src	breast:	n/a	chr19:44286386-44286397
13	CHD2	chr19:44286476-44287511	Hela-S3	cervix:	n/a	n/a
14	TAL1	chr19:44286458-44286715	K562	blood:	n/a	n/a
15	TBP	chr19:44286495-44287301	K562	blood:	n/a	n/a
16	MAX	chr19:44286439-44287482	Hela-S3	cervix:	n/a	n/a
17	PML	chr19:44284715-44286884	GM12878	blood:	n/a	n/a
18	E2F6	chr19:44286424-44287446	Hela-S3	cervix:	n/a	chr19:44287324-44287334 chr19:44287254-44287265
19	TCF3	chr19:44286439-44286707	GM12878	blood:	n/a	chr19:44286553-44286566
20	RCOR1	chr19:44286232-44287133	K562	blood:	n/a	n/a
21	RUNX3	chr19:44286278-44287303	GM12878	blood:	n/a	n/a
22	ELF1	chr19:44286509-44287322	GM12878	blood:	n/a	n/a
23	MAX	chr19:44284653-44287580	A549	lung:	n/a	n/a
24	FOS	chr19:44286365-44286565	MCF10A-Er-Src	breast:	n/a	chr19:44286386-44286397
25	POLR2A	chr19:44286275-44287458	GM12892	blood:	n/a	n/a
26	EGR1	chr19:44286413-44286744	K562	blood:	n/a	chr19:44286551-44286575 chr19:44286613-44286627 chr19:44286617-44286628
27	TFAP2C	chr19:44285948-44287558	Hela-S3	cervix:	n/a	n/a
28	NFIC	chr19:44286396-44286936	GM12878	blood:	n/a	n/a
29	MTA3	chr19:44284663-44287383	GM12878	blood:	n/a	n/a
30	STAT5A	chr19:44286481-44286776	GM12878	blood:	n/a	chr19:44286640-44286652
31	POLR2A	chr19:44286485-44287478	GM18505	blood:	n/a	n/a
32	TCF12	chr19:44286462-44286725	GM12878	blood:	n/a	n/a
33	MAX	chr19:44284808-44287558	HCT-116	colon:	n/a	n/a
34	TEAD4	chr19:44286330-44287034	K562	blood:	n/a	chr19:44286797-44286806
35	EGR1	chr19:44286489-44286680	GM12878	blood:	n/a	chr19:44286551-44286575 chr19:44286613-44286627 chr19:44286617-44286628
36	POLR2A	chr19:44286434-44287603	GM12892	blood:	n/a	n/a
37	MAX	chr19:44285845-44287442	K562	blood:	n/a	n/a
38	MYC	chr19:44286349-44287271	K562	blood:	n/a	n/a
39	MAX	chr19:44286499-44287302	K562	blood:	n/a	n/a
40	MAX	chr19:44286335-44287472	Hela-S3	cervix:	n/a	n/a
41	TCF3	chr19:44286486-44286793	GM12878	blood:	n/a	chr19:44286553-44286566
42	CBX3	chr19:44286227-44287098	K562	blood:	n/a	n/a
43	MYC	chr19:44286343-44287463	Hela-S3	cervix:	n/a	n/a
44	MAZ	chr19:44286474-44287358	K562	blood:	n/a	n/a
45	BHLHE40	chr19:44286455-44287299	K562	blood:	n/a	n/a
46	MYC	chr19:44286467-44286547	MCF10A-Er-Src	breast:	n/a	n/a

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:

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

Extended variants
information (count: 25 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10404672	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10404692	0.81[AMR][1000 genomes]
rs10405457	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10421887	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10422990	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11665924	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]
rs11669175	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11670158	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11671215	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12460161	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12463370	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12974061	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[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]
rs3760983	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760984	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802199	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802200	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803658	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60184524	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61138927	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[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

Variant related diseases (count:1)

Disease	PMID	Source
Breast cancer	23535729	GWAS catalog

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3760982	KDELR1	cis	parietal	SCAN
rs3760982	AC115522.3	cis	Skin Sun Exposed Lower leg	GTEx
rs3760982	ZNF404	trans	parietal	SCAN
rs3760982	KCNN4	cis	Whole Blood	GTEx
rs3760982	GEMIN7	cis	cerebellum	SCAN
rs3760982	ZNF296	cis	cerebellum	SCAN
rs3760982	ZNF296	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44281400-44287000	Enhancers	Spleen	Spleen
2	chr19:44282200-44286800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:44282400-44289200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:44284000-44288600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:44284200-44287800	Weak transcription	Dnd41	blood
6	chr19:44284400-44286600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr19:44284400-44287600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:44284400-44288400	Weak transcription	HUVEC	blood vessel
9	chr19:44285000-44287000	Enhancers	NHDF-Ad	bronchial
10	chr19:44285000-44287400	Flanking Active TSS	Primary B cells from peripheral blood	blood
11	chr19:44285200-44286800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:44285200-44287000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:44285200-44287400	Flanking Active TSS	GM12878-XiMat	blood
14	chr19:44285200-44289400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr19:44285200-44289400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr19:44285200-44289600	Enhancers	Esophagus	oesophagus
17	chr19:44285400-44286600	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr19:44285400-44286800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr19:44285400-44286800	Enhancers	Fetal Thymus	thymus
20	chr19:44285400-44287000	Enhancers	Primary T cells from cord blood	blood
21	chr19:44285400-44287000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:44285400-44287000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:44285400-44287200	Flanking Active TSS	Hela-S3	cervix
24	chr19:44285400-44287400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr19:44285400-44288600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:44285400-44288800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr19:44285400-44291400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr19:44285600-44286600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
29	chr19:44285600-44286600	Active TSS	Colonic Mucosa	Colon
30	chr19:44285600-44286600	Weak transcription	HepG2	liver
31	chr19:44285600-44286800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:44285600-44286800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:44285600-44287000	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr19:44285600-44288000	Weak transcription	Primary B cells from cord blood	blood
35	chr19:44285600-44288000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:44285600-44288600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr19:44285800-44286800	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr19:44285800-44287000	Enhancers	Placenta	Placenta
39	chr19:44285800-44287000	Enhancers	HMEC	breast
40	chr19:44285800-44287600	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr19:44285800-44288000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr19:44285800-44288000	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr19:44285800-44288200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr19:44285800-44288200	Enhancers	NHEK	skin
45	chr19:44285800-44288400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:44285800-44288400	Weak transcription	HSMMtube	muscle
47	chr19:44285800-44288600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr19:44285800-44288600	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr19:44285800-44289200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:44285800-44289400	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links