Variant report

Variant	rs56344893
Chromosome Location	chr19:44282529-44282530
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:44280377-44284435	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

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:

No data

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];0.97[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]
rs56681946	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];0.96[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
rs56344893	KCNN4	cis	Whole Blood	GTEx
rs56344893	AC115522.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:98 , 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	chr19:44279000-44282600	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr19:44279200-44283000	Weak transcription	Right Atrium	heart
6	chr19:44279200-44283200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr19:44279400-44282800	Enhancers	Stomach Mucosa	stomach
8	chr19:44279600-44283000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:44279800-44282800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:44279800-44283400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr19:44279800-44283600	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr19:44279800-44283600	Weak transcription	Small Intestine	intestine
13	chr19:44280200-44283000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:44280400-44282800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:44280600-44282800	Enhancers	Placenta	Placenta
16	chr19:44280600-44283200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:44280600-44284200	Enhancers	NHEK	skin
18	chr19:44280800-44283600	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr19:44280800-44284200	Weak transcription	Gastric	stomach
20	chr19:44280800-44284800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:44280800-44285800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr19:44281000-44283400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:44281000-44284600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr19:44281200-44283400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:44281200-44283800	Enhancers	NH-A	brain
26	chr19:44281200-44284400	Enhancers	HUVEC	blood vessel
27	chr19:44281200-44285600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:44281400-44282800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr19:44281400-44283000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr19:44281400-44283400	Enhancers	Brain Hippocampus Middle	brain
31	chr19:44281400-44283600	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr19:44281400-44287000	Enhancers	Spleen	Spleen
33	chr19:44281600-44282600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:44281600-44282600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:44281600-44283200	Enhancers	Brain Substantia Nigra	brain
36	chr19:44281600-44283400	Enhancers	Fetal Muscle Leg	muscle
37	chr19:44281800-44283000	Enhancers	Brain Cingulate Gyrus	brain
38	chr19:44281800-44283600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:44281800-44283800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr19:44281800-44284200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:44281800-44284400	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr19:44281800-44285400	Active TSS	Rectal Smooth Muscle	rectum
43	chr19:44281800-44285600	Enhancers	Fetal Intestine Large	intestine
44	chr19:44282000-44282800	Enhancers	Primary B cells from cord blood	blood
45	chr19:44282000-44282800	Enhancers	Primary B cells from peripheral blood	blood
46	chr19:44282000-44283200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:44282000-44283200	Enhancers	Esophagus	oesophagus
48	chr19:44282000-44283800	Enhancers	Adipose Nuclei	Adipose
49	chr19:44282000-44285600	Enhancers	Lung	lung
50	chr19:44282200-44282600	Enhancers	Hela-S3	cervix

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