Variant report

Variant	rs56681946
Chromosome Location	chr19:44283031-44283032
allele	C/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	NFIC	chr19:44282811-44283363	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:44280377-44284435	GM12878	blood:	n/a	n/a
3	STAT5A	chr19:44282730-44283830	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:44282657-44284379	HL-60	blood:	n/a	n/a
5	RCOR1	chr19:44282814-44284372	K562	blood:	n/a	n/a
6	WRNIP1	chr19:44282851-44284495	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:44282699-44284463	GM18505	blood:	n/a	n/a
8	CHD2	chr19:44282867-44284408	GM12878	blood:	n/a	n/a
9	PML	chr19:44282967-44284488	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:44282671-44284425	GM12891	blood:	n/a	n/a
11	POLR2A	chr19:44282566-44285595	GM12878	blood:	n/a	n/a
12	TBP	chr19:44282875-44283225	K562	blood:	n/a	n/a
13	MTA3	chr19:44282570-44284543	GM12878	blood:	n/a	n/a
14	ZEB1	chr19:44282838-44283185	GM12878	blood:	n/a	n/a
15	ATF3	chr19:44282903-44283324	K562	blood:	n/a	n/a
16	EBF1	chr19:44282787-44283071	GM12878	blood:	n/a	chr19:44282929-44282938 chr19:44282966-44282977
17	EBF1	chr19:44282727-44283736	GM12878	blood:	n/a	chr19:44282929-44282938 chr19:44282966-44282977
18	MAZ	chr19:44282922-44283122	K562	blood:	n/a	n/a
19	CHD1	chr19:44282816-44283729	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:44282833-44284373	GM19193	blood:	n/a	n/a
21	POLR2A	chr19:44282770-44284490	GM12878	blood:	n/a	n/a
22	EBF1	chr19:44282799-44283043	GM12878	blood:	n/a	chr19:44282929-44282938 chr19:44282966-44282977
23	RPC155	chr19:44282935-44283474	K562	blood:	n/a	n/a
24	TCF12	chr19:44282778-44283116	GM12878	blood:	n/a	n/a
25	ZEB1	chr19:44282856-44283057	GM12878	blood:	n/a	n/a
26	MAZ	chr19:44282811-44284539	GM12878	blood:	n/a	n/a
27	TCF12	chr19:44282781-44283106	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44228240..44229809-chr19:44281869..44283736,2	K562	blood:
2	chr19:44258057..44261358-chr19:44282388..44285287,3	MCF-7	breast:
3	chr19:44256760..44265122-chr19:44281375..44290996,18	K562	blood:
4	chr19:44270398..44273910-chr19:44281864..44284268,4	K562	blood:
5	chr19:44273760..44276209-chr19:44281232..44283359,2	MCF-7	breast:
6	chr19:44256077..44259725-chr19:44281509..44284317,6	MCF-7	breast:

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

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10401170	0.81[ASN][1000 genomes]
rs10401203	0.81[ASN][1000 genomes]
rs10426528	0.81[ASN][1000 genomes]
rs11083720	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11879798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs349046	0.81[ASN][1000 genomes]
rs349047	0.81[ASN][1000 genomes]
rs349048	0.81[ASN][1000 genomes]
rs56344893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62116961	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73048670	0.97[ASN][1000 genomes]
rs8104447	0.81[ASN][1000 genomes]
rs8111664	0.81[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
rs56681946	KCNN4	cis	Whole Blood	GTEx
rs56681946	AC115522.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44278200-44283800	Enhancers	Sigmoid Colon	Sigmoid Colon
2	chr19:44278800-44283200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:44278800-44283400	Enhancers	Placenta Amnion	Placenta Amnion
4	chr19:44279200-44283200	Enhancers	Primary T cells fromperipheralblood	blood
5	chr19:44279800-44283400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr19:44279800-44283600	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr19:44279800-44283600	Weak transcription	Small Intestine	intestine
8	chr19:44280600-44283200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:44280600-44284200	Enhancers	NHEK	skin
10	chr19:44280800-44283600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr19:44280800-44284200	Weak transcription	Gastric	stomach
12	chr19:44280800-44284800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:44280800-44285800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr19:44281000-44283400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:44281000-44284600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr19:44281200-44283400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:44281200-44283800	Enhancers	NH-A	brain
18	chr19:44281200-44284400	Enhancers	HUVEC	blood vessel
19	chr19:44281200-44285600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:44281400-44283400	Enhancers	Brain Hippocampus Middle	brain
21	chr19:44281400-44283600	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr19:44281400-44287000	Enhancers	Spleen	Spleen
23	chr19:44281600-44283200	Enhancers	Brain Substantia Nigra	brain
24	chr19:44281600-44283400	Enhancers	Fetal Muscle Leg	muscle
25	chr19:44281800-44283600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:44281800-44283800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr19:44281800-44284200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:44281800-44284400	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr19:44281800-44285400	Active TSS	Rectal Smooth Muscle	rectum
30	chr19:44281800-44285600	Enhancers	Fetal Intestine Large	intestine
31	chr19:44282000-44283200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:44282000-44283200	Enhancers	Esophagus	oesophagus
33	chr19:44282000-44283800	Enhancers	Adipose Nuclei	Adipose
34	chr19:44282000-44285600	Enhancers	Lung	lung
35	chr19:44282200-44283200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr19:44282200-44283200	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr19:44282200-44283400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:44282200-44283400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:44282200-44283400	Weak transcription	Fetal Intestine Small	intestine
40	chr19:44282200-44283400	Weak transcription	Osteobl	bone
41	chr19:44282200-44283600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:44282200-44283600	Enhancers	A549	lung
43	chr19:44282200-44283600	Weak transcription	HSMM	muscle
44	chr19:44282200-44284800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr19:44282200-44286800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:44282400-44283200	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr19:44282400-44283400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:44282400-44283400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:44282400-44283600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:44282400-44283600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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