Variant report

Variant	rs3760984
Chromosome Location	chr19:44286762-44286763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 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	RCOR1	chr19:44286352-44286809	K562	blood:	n/a	n/a
3	JUND	chr19:44286524-44287147	K562	blood:	n/a	n/a
4	NR2C2	chr19:44285391-44287077	GM12878	blood:	n/a	n/a
5	ZC3H11A	chr19:44286650-44286932	K562	blood:	n/a	n/a
6	RELA	chr19:44286496-44287320	GM19193	blood:	n/a	n/a
7	POLR2A	chr19:44286719-44287169	GM12878	blood:	n/a	n/a
8	MAX	chr19:44286401-44287086	K562	blood:	n/a	n/a
9	RUNX3	chr19:44286289-44287308	GM12878	blood:	n/a	n/a
10	EP300	chr19:44286447-44287285	K562	blood:	n/a	n/a
11	RCOR1	chr19:44286456-44287483	Hela-S3	cervix:	n/a	n/a
12	CHD2	chr19:44286476-44287511	Hela-S3	cervix:	n/a	n/a
13	MXI1	chr19:44286761-44287479	Hela-S3	cervix:	n/a	n/a
14	TBP	chr19:44286495-44287301	K562	blood:	n/a	n/a
15	MAX	chr19:44286439-44287482	Hela-S3	cervix:	n/a	n/a
16	TFAP2A	chr19:44286655-44287484	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	RCOR1	chr19:44286232-44287133	K562	blood:	n/a	n/a
20	POLR2A	chr19:44286743-44287031	Hela-S3	cervix:	n/a	n/a
21	E2F6	chr19:44286536-44287464	K562	blood:	n/a	chr19:44287324-44287334 chr19:44287254-44287265
22	POLR2A	chr19:44286734-44287561	Hela-S3	cervix:	n/a	n/a
23	MAZ	chr19:44286678-44287487	Hela-S3	cervix:	n/a	n/a
24	RUNX3	chr19:44286278-44287303	GM12878	blood:	n/a	n/a
25	ELF1	chr19:44286509-44287322	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:44286711-44287018	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr19:44286597-44287543	Hela-S3	cervix:	n/a	n/a
28	MAX	chr19:44284653-44287580	A549	lung:	n/a	n/a
29	POLR2A	chr19:44286275-44287458	GM12892	blood:	n/a	n/a
30	TFAP2C	chr19:44285948-44287558	Hela-S3	cervix:	n/a	n/a
31	NFIC	chr19:44286396-44286936	GM12878	blood:	n/a	n/a
32	MTA3	chr19:44284663-44287383	GM12878	blood:	n/a	n/a
33	STAT5A	chr19:44286481-44286776	GM12878	blood:	n/a	chr19:44286640-44286652
34	POLR2A	chr19:44286485-44287478	GM18505	blood:	n/a	n/a
35	MAX	chr19:44284808-44287558	HCT-116	colon:	n/a	n/a
36	TEAD4	chr19:44286330-44287034	K562	blood:	n/a	chr19:44286797-44286806
37	MAZ	chr19:44286569-44286775	GM12878	blood:	n/a	n/a
38	MYC	chr19:44286752-44287417	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr19:44286434-44287603	GM12892	blood:	n/a	n/a
40	TCF7L2	chr19:44286603-44287481	Hela-S3	cervix:	n/a	n/a
41	MAX	chr19:44285845-44287442	K562	blood:	n/a	n/a
42	MYC	chr19:44286349-44287271	K562	blood:	n/a	n/a
43	MAX	chr19:44286499-44287302	K562	blood:	n/a	n/a
44	MAX	chr19:44286335-44287472	Hela-S3	cervix:	n/a	n/a
45	TCF3	chr19:44286486-44286793	GM12878	blood:	n/a	chr19:44286553-44286566
46	CBX3	chr19:44286227-44287098	K562	blood:	n/a	n/a
47	MYC	chr19:44286343-44287463	Hela-S3	cervix:	n/a	n/a
48	MAZ	chr19:44286474-44287358	K562	blood:	n/a	n/a
49	BHLHE40	chr19:44286455-44287299	K562	blood:	n/a	n/a
50	CHD2	chr19:44286666-44286889	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: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10404672	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10404692	0.82[AMR][1000 genomes]
rs10405457	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10421887	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10422990	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11665924	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11669175	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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];0.88[ASN][1000 genomes]
rs12460161	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12463370	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12974061	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3760982	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760983	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802199	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802200	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803658	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60184524	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61138927	0.93[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3760984	KCNN4	cis	Whole Blood	GTEx
rs3760984	AC115522.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:77 , 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	chr19:44284400-44287600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:44284400-44288400	Weak transcription	HUVEC	blood vessel
8	chr19:44285000-44287000	Enhancers	NHDF-Ad	bronchial
9	chr19:44285000-44287400	Flanking Active TSS	Primary B cells from peripheral blood	blood
10	chr19:44285200-44286800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:44285200-44287000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:44285200-44287400	Flanking Active TSS	GM12878-XiMat	blood
13	chr19:44285200-44289400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr19:44285200-44289400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:44285200-44289600	Enhancers	Esophagus	oesophagus
16	chr19:44285400-44286800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr19:44285400-44286800	Enhancers	Fetal Thymus	thymus
18	chr19:44285400-44287000	Enhancers	Primary T cells from cord blood	blood
19	chr19:44285400-44287000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr19:44285400-44287000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:44285400-44287200	Flanking Active TSS	Hela-S3	cervix
22	chr19:44285400-44287400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr19:44285400-44288600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr19:44285400-44288800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:44285400-44291400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:44285600-44286800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:44285600-44286800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:44285600-44287000	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr19:44285600-44288000	Weak transcription	Primary B cells from cord blood	blood
30	chr19:44285600-44288000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr19:44285600-44288600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr19:44285800-44286800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr19:44285800-44287000	Enhancers	Placenta	Placenta
34	chr19:44285800-44287000	Enhancers	HMEC	breast
35	chr19:44285800-44287600	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr19:44285800-44288000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr19:44285800-44288000	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr19:44285800-44288200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr19:44285800-44288200	Enhancers	NHEK	skin
40	chr19:44285800-44288400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:44285800-44288400	Weak transcription	HSMMtube	muscle
42	chr19:44285800-44288600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr19:44285800-44288600	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr19:44285800-44289200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:44285800-44289400	Enhancers	Stomach Mucosa	stomach
46	chr19:44285800-44289800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr19:44286000-44286800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr19:44286000-44287000	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr19:44286000-44287200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:44286000-44287800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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