Variant report

Variant	rs62116961
Chromosome Location	chr19:44283843-44283844
allele	C/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	MAX	chr19:44283305-44284355	NB4	blood:	n/a	n/a
2	RCOR1	chr19:44283683-44284310	K562	blood:	n/a	n/a
3	CTCF	chr19:44283519-44285246	A549	lung:	n/a	chr19:44284329-44284338 chr19:44284213-44284226
4	GATA3	chr19:44283374-44283930	MCF-7	breast:	n/a	chr19:44283719-44283729
5	POLR2A	chr19:44280377-44284435	GM12878	blood:	n/a	n/a
6	BCLAF1	chr19:44283702-44284374	GM12878	blood:	n/a	n/a
7	FOS	chr19:44283560-44284239	MCF10A-Er-Src	breast:	n/a	chr19:44283868-44283876 chr19:44283883-44283893 chr19:44283883-44283893
8	POLR2A	chr19:44282657-44284379	HL-60	blood:	n/a	n/a
9	NFIC	chr19:44283786-44284415	GM12878	blood:	n/a	n/a
10	RCOR1	chr19:44282814-44284372	K562	blood:	n/a	n/a
11	POLR2A	chr19:44283214-44284391	HL-60	blood:	n/a	n/a
12	WRNIP1	chr19:44282851-44284495	GM12878	blood:	n/a	n/a
13	TCF12	chr19:44283560-44284513	A549	lung:	n/a	n/a
14	POLR2A	chr19:44282699-44284463	GM18505	blood:	n/a	n/a
15	CHD2	chr19:44282867-44284408	GM12878	blood:	n/a	n/a
16	NR2F2	chr19:44283564-44284425	MCF-7	breast:	n/a	n/a
17	PML	chr19:44282967-44284488	GM12878	blood:	n/a	n/a
18	RUNX3	chr19:44283705-44284371	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:44282671-44284425	GM12891	blood:	n/a	n/a
20	POLR2A	chr19:44283508-44284586	HCT-116	colon:	n/a	n/a
21	POLR2A	chr19:44282566-44285595	GM12878	blood:	n/a	n/a
22	MYC	chr19:44283420-44284260	MCF10A-Er-Src	breast:	n/a	n/a
23	FOS	chr19:44283650-44283942	MCF10A-Er-Src	breast:	n/a	chr19:44283868-44283876 chr19:44283883-44283893 chr19:44283883-44283893
24	TCF7L2	chr19:44283611-44284379	Hela-S3	cervix:	n/a	n/a
25	MYC	chr19:44283317-44283865	MCF10A-Er-Src	breast:	n/a	n/a
26	MAZ	chr19:44283665-44284427	K562	blood:	n/a	n/a
27	CEBPB	chr19:44283565-44283850	Hela-S3	cervix:	n/a	n/a
28	MTA3	chr19:44282570-44284543	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:44283197-44283934	GM12892	blood:	n/a	n/a
30	STAT3	chr19:44283762-44283849	MCF10A-Er-Src	breast:	n/a	n/a
31	NFATC1	chr19:44283470-44283964	GM12878	blood:	n/a	n/a
32	POLR2A	chr19:44282833-44284373	GM19193	blood:	n/a	n/a
33	POLR2A	chr19:44282770-44284490	GM12878	blood:	n/a	n/a
34	MXI1	chr19:44283300-44284406	GM12878	blood:	n/a	n/a
35	MAZ	chr19:44283654-44284324	Hela-S3	cervix:	n/a	n/a
36	GATA3	chr19:44283557-44284178	MCF-7	breast:	n/a	chr19:44283719-44283729
37	MAZ	chr19:44282811-44284539	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44258057..44261358-chr19:44282388..44285287,3	MCF-7	breast:
2	chr19:44269561..44270470-chr19:44283736..44284661,2	MCF-7	breast:
3	chr19:44259347..44259872-chr19:44283284..44283854,2	NB4	blood:
4	chr19:44256760..44265122-chr19:44281375..44290996,18	K562	blood:
5	chr19:44270398..44273910-chr19:44281864..44284268,4	K562	blood:
6	chr19:44270615..44271921-chr19:44283761..44284756,6	MCF-7	breast:
7	chr19:44270285..44271265-chr19:44283659..44284189,2	K562	blood:
8	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: 6 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11083720	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11879798	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56344893	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56681946	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73048670	0.93[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
rs62116961	KCNN4	cis	Whole Blood	GTEx
rs62116961	AC115522.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44280600-44284200	Enhancers	NHEK	skin
2	chr19:44280800-44284200	Weak transcription	Gastric	stomach
3	chr19:44280800-44284800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:44280800-44285800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr19:44281000-44284600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr19:44281200-44284400	Enhancers	HUVEC	blood vessel
7	chr19:44281200-44285600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:44281400-44287000	Enhancers	Spleen	Spleen
9	chr19:44281800-44284200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:44281800-44284400	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr19:44281800-44285400	Active TSS	Rectal Smooth Muscle	rectum
12	chr19:44281800-44285600	Enhancers	Fetal Intestine Large	intestine
13	chr19:44282000-44285600	Enhancers	Lung	lung
14	chr19:44282200-44284800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr19:44282200-44286800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:44282400-44284200	Enhancers	Dnd41	blood
17	chr19:44282400-44284800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr19:44282400-44285000	Weak transcription	NHDF-Ad	bronchial
19	chr19:44282400-44289200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr19:44282600-44284000	Flanking Active TSS	GM12878-XiMat	blood
21	chr19:44282600-44284200	Flanking Active TSS	Hela-S3	cervix
22	chr19:44282600-44284400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr19:44282600-44284400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr19:44282600-44284400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr19:44282600-44284600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:44282800-44284000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr19:44282800-44284200	Flanking Active TSS	Primary B cells from peripheral blood	blood
28	chr19:44282800-44284400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr19:44282800-44284400	Flanking Active TSS	Thymus	Thymus
30	chr19:44282800-44284400	Flanking Active TSS	K562	blood
31	chr19:44282800-44284600	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr19:44282800-44284600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr19:44282800-44285800	Flanking Active TSS	Placenta	Placenta
34	chr19:44283000-44284400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:44283000-44284400	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr19:44283000-44284600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr19:44283000-44284600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr19:44283000-44284800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr19:44283000-44285000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:44283000-44285200	Flanking Active TSS	Colonic Mucosa	Colon
41	chr19:44283000-44285400	Flanking Active TSS	Fetal Thymus	thymus
42	chr19:44283000-44286000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:44283200-44284000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr19:44283200-44284000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:44283200-44284200	Weak transcription	Right Atrium	heart
46	chr19:44283200-44284400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:44283200-44284600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr19:44283200-44284600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr19:44283200-44285000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr19:44283200-44285600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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