Variant report

Variant	rs4802200
Chromosome Location	chr19:44289518-44289519
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	TAF1	chr19:44289429-44289705	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr19:44289372-44289796	H1-hESC	embryonic stem cell:	n/a	chr19:44289629-44289650 chr19:44289641-44289648 chr19:44289409-44289422 chr19:44289634-44289652
3	POLR2A	chr19:44289471-44289589	A549	lung:	n/a	n/a
4	NFIC	chr19:44289413-44289762	HepG2	liver:	n/a	chr19:44289686-44289702 chr19:44289685-44289702
5	CTCF	chr19:44289518-44289809	ECC-1	luminal epithelium:	n/a	chr19:44289629-44289650 chr19:44289641-44289648 chr19:44289634-44289652
6	REST	chr19:44289311-44289863	PFSK-1	brain:	n/a	n/a
7	FOS	chr19:44289355-44289804	MCF10A-Er-Src	breast:	n/a	n/a
8	NR2F2	chr19:44289186-44289812	MCF-7	breast:	n/a	chr19:44289484-44289499
9	YY1	chr19:44289367-44289823	GM12878	blood:	n/a	chr19:44289585-44289597 chr19:44289587-44289595
10	RAD21	chr19:44289422-44289769	GM12878	blood:	n/a	chr19:44289632-44289651
11	RAD21	chr19:44289502-44289744	K562	blood:	n/a	chr19:44289632-44289651
12	E2F6	chr19:44289450-44289630	K562	blood:	n/a	n/a
13	TCF7L2	chr19:44289285-44289744	Hela-S3	cervix:	n/a	n/a
14	REST	chr19:44289485-44289759	H1-hESC	embryonic stem cell:	n/a	n/a
15	REST	chr19:44289329-44289806	MCF-7	breast:	n/a	n/a
16	SMC3	chr19:44288534-44289891	SK-N-SH	brain:	n/a	chr19:44289636-44289650
17	ZNF217	chr19:44289292-44289722	MCF-7	breast:	n/a	n/a
18	MTA3	chr19:44288954-44289855	GM12878	blood:	n/a	n/a
19	CTCF	chr19:44289498-44289808	HUVEC	blood vessel:	n/a	chr19:44289629-44289650 chr19:44289641-44289648 chr19:44289634-44289652
20	YY1	chr19:44289383-44289720	H1-hESC	embryonic stem cell:	n/a	chr19:44289585-44289597 chr19:44289587-44289595
21	CTCF	chr19:44289406-44289905	HCT-116	colon:	n/a	chr19:44289629-44289650 chr19:44289641-44289648 chr19:44289409-44289422 chr19:44289634-44289652
22	UBTF	chr19:44289332-44289729	K562	blood:	n/a	n/a
23	MAFK	chr19:44289433-44289858	Hela-S3	cervix:	n/a	n/a
24	RUNX3	chr19:44289383-44289787	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:44289426-44289768	K562	blood:	n/a	n/a
26	EP300	chr19:44289468-44289769	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr19:44289106-44290134	A549	lung:	n/a	chr19:44289629-44289650 chr19:44289641-44289648 chr19:44289409-44289422 chr19:44289634-44289652
28	TBL1XR1	chr19:44289330-44289708	K562	blood:	n/a	n/a
29	RAD21	chr19:44289226-44289941	MCF-7	breast:	n/a	chr19:44289632-44289651
30	STAT5A	chr19:44289462-44289755	GM12878	blood:	n/a	chr19:44289518-44289530
31	STAT3	chr19:44289482-44289553	MCF10A-Er-Src	breast:	n/a	chr19:44289518-44289530
32	RFX5	chr19:44289405-44289827	Hela-S3	cervix:	n/a	n/a
33	CTCF	chr19:44289506-44289781	A549	lung:	n/a	chr19:44289629-44289650 chr19:44289641-44289648 chr19:44289634-44289652
34	REST	chr19:44289255-44289847	A549	lung:	n/a	n/a
35	REST	chr19:44289443-44289822	K562	blood:	n/a	n/a
36	YY1	chr19:44289276-44289810	H1-hESC	embryonic stem cell:	n/a	chr19:44289585-44289597 chr19:44289587-44289595
37	ZNF143	chr19:44289449-44289828	K562	blood:	n/a	n/a
38	ZMIZ1	chr19:44289466-44289787	K562	blood:	n/a	n/a
39	TCF7L2	chr19:44289207-44289694	PANC-1	pancreas:	n/a	n/a
40	RAD21	chr19:44289380-44289812	HepG2	liver:	n/a	chr19:44289632-44289651
41	GATA3	chr19:44289151-44289815	MCF-7	breast:	n/a	chr19:44289411-44289421
42	TCF12	chr19:44288283-44289988	MCF-7	breast:	n/a	chr19:44288708-44288715
43	E2F6	chr19:44289135-44289890	A549	lung:	n/a	n/a
44	RAD21	chr19:44288143-44290075	HCT-116	colon:	n/a	chr19:44288672-44288682 chr19:44289632-44289651
45	SIN3AK20	chr19:44289477-44289786	SK-N-SH	brain:	n/a	n/a
46	RUNX3	chr19:44289374-44289824	GM12878	blood:	n/a	n/a
47	RCOR1	chr19:44289286-44289819	K562	blood:	n/a	n/a
48	SIN3AK20	chr19:44288363-44289941	MCF-7	breast:	n/a	n/a
49	CTCF	chr19:44289483-44289798	ECC-1	luminal epithelium:	n/a	chr19:44289629-44289650 chr19:44289641-44289648 chr19:44289634-44289652
50	POLR2A	chr19:44289211-44289819	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44254856..44260610-chr19:44285479..44289743,8	MCF-7	breast:
2	chr19:44249057..44250070-chr19:44289173..44290085,5	K562	blood:
3	chr19:44248925..44250090-chr19:44289091..44290176,10	MCF-7	breast:
4	chr19:44248044..44248800-chr19:44289490..44290112,3	K562	blood:
5	chr19:44270617..44271581-chr19:44289245..44290116,2	MCF-7	breast:
6	chr19:44037281..44039805-chr19:44287429..44289593,2	K562	blood:
7	chr19:43967500..43969727-chr19:44288135..44290383,3	MCF-7	breast:
8	chr19:44250536..44251488-chr19:44288767..44289640,2	MCF-7	breast:
9	chr19:44270260..44271258-chr19:44289187..44290070,3	K562	blood:
10	chr19:44256760..44265122-chr19:44281375..44290996,18	K562	blood:
11	chr19:44256245..44259869-chr19:44284477..44291035,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNN4-1	chr19:44289294-44290302	XLOC_013347

Variant related genes	Relation type
KCNN4	TF binding region
ENSG00000124466	Chromatin interaction
ENSG00000105771	Chromatin interaction
ENSG00000176472	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10404672	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10405457	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10421887	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10422990	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11665924	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11669175	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670158	0.84[EUR][1000 genomes]
rs11671215	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12460161	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12463370	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12974061	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3760982	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760983	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760984	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802199	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803658	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803659	0.88[AFR][1000 genomes]
rs60184524	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61013802	0.85[AFR][1000 genomes]
rs61138927	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[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
rs4802200	KCNN4	cis	Whole Blood	GTEx
rs4802200	AC115522.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44285200-44289600	Enhancers	Esophagus	oesophagus
2	chr19:44285400-44291400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:44285800-44289800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:44286000-44289600	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr19:44286600-44289800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr19:44287400-44289600	Enhancers	Colonic Mucosa	Colon
7	chr19:44287400-44289800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr19:44287400-44289800	Enhancers	Duodenum Mucosa	Duodenum
9	chr19:44287400-44291400	Enhancers	HMEC	breast
10	chr19:44287600-44289800	Flanking Active TSS	Hela-S3	cervix
11	chr19:44287800-44289600	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr19:44287800-44289600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:44287800-44289600	Enhancers	Fetal Thymus	thymus
14	chr19:44288000-44289600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:44288000-44289600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr19:44288000-44289600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr19:44288000-44289600	Enhancers	Primary B cells from cord blood	blood
18	chr19:44288000-44289600	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr19:44288000-44290200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:44288200-44289600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr19:44288200-44289600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr19:44288200-44289600	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr19:44288200-44289600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr19:44288200-44289600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:44288200-44289600	Flanking Active TSS	A549	lung
26	chr19:44288200-44289600	Enhancers	HSMM	muscle
27	chr19:44288200-44289600	Flanking Active TSS	NHEK	skin
28	chr19:44288400-44289600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr19:44288400-44289600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:44288400-44289600	Enhancers	Adipose Nuclei	Adipose
31	chr19:44288400-44289600	Enhancers	HSMMtube	muscle
32	chr19:44288400-44289600	Enhancers	HUVEC	blood vessel
33	chr19:44288400-44289600	Flanking Active TSS	K562	blood
34	chr19:44288400-44289800	Enhancers	Primary B cells from peripheral blood	blood
35	chr19:44288400-44289800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
36	chr19:44288400-44289800	Enhancers	Placenta	Placenta
37	chr19:44288400-44290200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr19:44288600-44289600	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr19:44288600-44289600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr19:44288600-44289600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:44288600-44289600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr19:44288600-44289600	Flanking Active TSS	Dnd41	blood
43	chr19:44288600-44289800	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr19:44288800-44289600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr19:44288800-44289600	Enhancers	GM12878-XiMat	blood
46	chr19:44288800-44290200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr19:44289000-44289600	Enhancers	Colon Smooth Muscle	Colon
48	chr19:44289000-44289600	Enhancers	Fetal Muscle Leg	muscle
49	chr19:44289000-44289600	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr19:44289000-44289600	Enhancers	Spleen	Spleen

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