Variant report

Variant	rs11083720
Chromosome Location	chr19:44281492-44281493
allele	G/T
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	IKZF1	chr19:44280867-44282384	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:44281360-44282438	HL-60	blood:	n/a	n/a
3	POLR2A	chr19:44280646-44282428	GM12891	blood:	n/a	n/a
4	TEAD4	chr19:44281202-44282204	K562	blood:	n/a	chr19:44281401-44281410
5	POLR2A	chr19:44281490-44281842	K562	blood:	n/a	n/a
6	RUNX3	chr19:44281204-44282400	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:44280377-44284435	GM12878	blood:	n/a	n/a
8	NFIC	chr19:44281460-44282350	SK-N-SH	brain:	n/a	n/a
9	FOXM1	chr19:44281425-44282424	GM12878	blood:	n/a	n/a
10	MAZ	chr19:44281309-44282288	K562	blood:	n/a	n/a
11	BCLAF1	chr19:44281110-44282330	GM12878	blood:	n/a	chr19:44281806-44281815
12	USF1	chr19:44281284-44281717	K562	blood:	n/a	n/a
13	WRNIP1	chr19:44280528-44282364	GM12878	blood:	n/a	n/a
14	ZNF384	chr19:44281339-44282338	K562	blood:	n/a	n/a
15	RCOR1	chr19:44281312-44282295	K562	blood:	n/a	n/a
16	TCF12	chr19:44281338-44282165	SK-N-SH	brain:	n/a	chr19:44282019-44282029
17	JUND	chr19:44281426-44282306	K562	blood:	n/a	chr19:44281637-44281645 chr19:44281633-44281644 chr19:44282283-44282297
18	MYC	chr19:44281315-44282228	K562	blood:	n/a	n/a
19	FOXM1	chr19:44281306-44282122	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:44281029-44281815	GM12878	blood:	n/a	n/a
21	ZBTB7A	chr19:44281480-44281909	K562	blood:	n/a	chr19:44281523-44281532
22	MAZ	chr19:44281310-44282340	GM12878	blood:	n/a	n/a
23	MTA3	chr19:44281255-44281771	GM12878	blood:	n/a	n/a
24	FOSL2	chr19:44281333-44282018	SK-N-SH	brain:	n/a	chr19:44281637-44281645 chr19:44281633-44281644
25	POLR2A	chr19:44281467-44281876	K562	blood:	n/a	n/a
26	MAX	chr19:44281225-44281743	GM12878	blood:	n/a	n/a
27	CHD2	chr19:44281350-44282304	GM12878	blood:	n/a	n/a
28	BHLHE40	chr19:44281291-44282278	K562	blood:	n/a	n/a
29	POLR2A	chr19:44281357-44282295	HCT-116	colon:	n/a	n/a
30	TAF1	chr19:44281137-44281505	GM12878	blood:	n/a	n/a
31	EP300	chr19:44281474-44282283	SK-N-SH_RA	brain:	n/a	chr19:44281830-44281844 chr19:44282264-44282278 chr19:44281821-44281835 chr19:44282268-44282277
32	EP300	chr19:44281244-44282259	K562	blood:	n/a	chr19:44281830-44281844 chr19:44281821-44281835
33	EP300	chr19:44281372-44282240	SK-N-SH	brain:	n/a	chr19:44281830-44281844 chr19:44281821-44281835
34	EP300	chr19:44281241-44282338	GM12878	blood:	n/a	chr19:44281830-44281844 chr19:44282264-44282278 chr19:44281821-44281835 chr19:44282268-44282277
35	MAFF	chr19:44281428-44281561	K562	blood:	n/a	n/a
36	EP300	chr19:44281480-44281896	SK-N-SH_RA	brain:	n/a	chr19:44281830-44281844 chr19:44281821-44281835
37	RUNX3	chr19:44281123-44282371	GM12878	blood:	n/a	n/a
38	RCOR1	chr19:44281316-44282371	GM12878	blood:	n/a	n/a
39	POLR2A	chr19:44281001-44281802	GM12878	blood:	n/a	n/a
40	NFIC	chr19:44281475-44282264	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr19:44281311-44282362	GM12878	blood:	n/a	n/a
42	POLR2A	chr19:44281285-44281541	GM12878	blood:	n/a	n/a
43	TEAD4	chr19:44281174-44281814	K562	blood:	n/a	chr19:44281401-44281410
44	ARID3A	chr19:44281426-44281604	K562	blood:	n/a	n/a
45	STAT5A	chr19:44281378-44282449	GM12878	blood:	n/a	chr19:44281529-44281541
46	EBF1	chr19:44281374-44281818	GM12878	blood:	n/a	chr19:44281512-44281523
47	RCOR1	chr19:44281329-44282305	K562	blood:	n/a	n/a
48	NFIC	chr19:44281326-44282350	GM12878	blood:	n/a	n/a
49	POLR2A	chr19:44281241-44281787	GM12892	blood:	n/a	n/a
50	TBL1XR1	chr19:44281420-44281907	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44091165..44093926-chr19:44279180..44281985,2	K562	blood:
2	chr19:44256760..44265122-chr19:44281375..44290996,18	K562	blood:
3	chr19:44273760..44276209-chr19:44281232..44283359,2	MCF-7	breast:

Variant related genes	Relation type
KCNN4	TF binding region
ENSG00000105771	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000104783	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11879798	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56344893	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56681946	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62116961	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73048670	0.89[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
rs11083720	KCNN4	cis	Whole Blood	GTEx
rs11083720	AC115522.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44278200-44281800	Enhancers	Primary hematopoietic stem cells	blood
2	chr19:44278200-44283800	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr19:44278800-44281800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:44278800-44282000	Weak transcription	Esophagus	oesophagus
5	chr19:44278800-44283200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:44278800-44283400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr19:44279000-44282600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr19:44279200-44281600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:44279200-44281600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:44279200-44281600	Weak transcription	Brain Substantia Nigra	brain
11	chr19:44279200-44281600	Enhancers	Colonic Mucosa	Colon
12	chr19:44279200-44281800	Enhancers	Duodenum Mucosa	Duodenum
13	chr19:44279200-44281800	Weak transcription	Osteobl	bone
14	chr19:44279200-44283000	Weak transcription	Right Atrium	heart
15	chr19:44279200-44283200	Enhancers	Primary T cells fromperipheralblood	blood
16	chr19:44279400-44282800	Enhancers	Stomach Mucosa	stomach
17	chr19:44279600-44281600	Enhancers	Primary B cells from cord blood	blood
18	chr19:44279600-44281600	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr19:44279600-44281600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr19:44279600-44281600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:44279600-44282000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:44279600-44282000	Weak transcription	NHDF-Ad	bronchial
23	chr19:44279600-44283000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:44279800-44281800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr19:44279800-44281800	Enhancers	Fetal Thymus	thymus
26	chr19:44279800-44281800	Weak transcription	HSMM	muscle
27	chr19:44279800-44282800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:44279800-44283400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr19:44279800-44283600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr19:44279800-44283600	Weak transcription	Small Intestine	intestine
31	chr19:44280000-44281800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:44280200-44281600	Enhancers	A549	lung
33	chr19:44280200-44283000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr19:44280400-44282400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr19:44280400-44282400	Flanking Active TSS	GM12878-XiMat	blood
36	chr19:44280400-44282800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:44280600-44281600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr19:44280600-44281600	Weak transcription	Fetal Intestine Small	intestine
39	chr19:44280600-44281800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr19:44280600-44282400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:44280600-44282800	Enhancers	Placenta	Placenta
42	chr19:44280600-44283200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:44280600-44284200	Enhancers	NHEK	skin
44	chr19:44280800-44281600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:44280800-44281600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:44280800-44281600	Enhancers	Thymus	Thymus
47	chr19:44280800-44282000	Weak transcription	Lung	lung
48	chr19:44280800-44282400	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr19:44280800-44282400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:44280800-44283600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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