Variant report

Variant	rs11879798
Chromosome Location	chr19:44281898-44281899
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	IKZF1	chr19:44280867-44282384	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:44281798-44282324	GM12891	blood:	n/a	n/a
3	MAFK	chr19:44281509-44281988	K562	blood:	n/a	n/a
4	POLR2A	chr19:44281360-44282438	HL-60	blood:	n/a	n/a
5	POLR2A	chr19:44280646-44282428	GM12891	blood:	n/a	n/a
6	TEAD4	chr19:44281202-44282204	K562	blood:	n/a	chr19:44281401-44281410
7	EP300	chr19:44281503-44282303	GM12878	blood:	n/a	chr19:44281830-44281844 chr19:44282264-44282278 chr19:44281821-44281835 chr19:44282268-44282277
8	ZC3H11A	chr19:44281756-44282341	K562	blood:	n/a	n/a
9	RUNX3	chr19:44281204-44282400	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:44280377-44284435	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:44281596-44282320	GM12878	blood:	n/a	n/a
12	RAD21	chr19:44281587-44281926	SK-N-SH_RA	brain:	n/a	chr19:44281664-44281676
13	NFIC	chr19:44281460-44282350	SK-N-SH	brain:	n/a	n/a
14	MAX	chr19:44281578-44282307	NB4	blood:	n/a	n/a
15	FOXM1	chr19:44281425-44282424	GM12878	blood:	n/a	n/a
16	MAZ	chr19:44281309-44282288	K562	blood:	n/a	n/a
17	BCLAF1	chr19:44281110-44282330	GM12878	blood:	n/a	chr19:44281806-44281815
18	CEBPB	chr19:44281810-44282040	K562	blood:	n/a	n/a
19	WRNIP1	chr19:44280528-44282364	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:44281889-44282367	GM12891	blood:	n/a	n/a
21	TCF12	chr19:44281841-44282242	GM12878	blood:	n/a	chr19:44282019-44282029
22	POLR2A	chr19:44281635-44282027	HCT-116	colon:	n/a	n/a
23	ZNF384	chr19:44281339-44282338	K562	blood:	n/a	n/a
24	POLR2A	chr19:44281500-44282444	HL-60	blood:	n/a	n/a
25	RCOR1	chr19:44281312-44282295	K562	blood:	n/a	n/a
26	TCF12	chr19:44281338-44282165	SK-N-SH	brain:	n/a	chr19:44282019-44282029
27	JUND	chr19:44281426-44282306	K562	blood:	n/a	chr19:44281637-44281645 chr19:44281633-44281644 chr19:44282283-44282297
28	MYC	chr19:44281315-44282228	K562	blood:	n/a	n/a
29	FOXM1	chr19:44281306-44282122	GM12878	blood:	n/a	n/a
30	CTCF	chr19:44281674-44281935	K562	blood:	n/a	n/a
31	ZBTB7A	chr19:44281480-44281909	K562	blood:	n/a	chr19:44281523-44281532
32	MAZ	chr19:44281310-44282340	GM12878	blood:	n/a	n/a
33	SPI1	chr19:44281578-44282406	HL-60	blood:	n/a	chr19:44282165-44282178
34	PML	chr19:44281577-44282484	GM12878	blood:	n/a	n/a
35	FOSL2	chr19:44281333-44282018	SK-N-SH	brain:	n/a	chr19:44281637-44281645 chr19:44281633-44281644
36	BHLHE40	chr19:44281876-44282383	GM12878	blood:	n/a	n/a
37	TBL1XR1	chr19:44281619-44282230	K562	blood:	n/a	n/a
38	CHD2	chr19:44281350-44282304	GM12878	blood:	n/a	n/a
39	ZMIZ1	chr19:44281546-44282145	K562	blood:	n/a	n/a
40	BHLHE40	chr19:44281291-44282278	K562	blood:	n/a	n/a
41	POLR2A	chr19:44281357-44282295	HCT-116	colon:	n/a	n/a
42	CTCF	chr19:44281870-44282070	GM12878	blood:	n/a	n/a
43	EP300	chr19:44281474-44282283	SK-N-SH_RA	brain:	n/a	chr19:44281830-44281844 chr19:44282264-44282278 chr19:44281821-44281835 chr19:44282268-44282277
44	EP300	chr19:44281244-44282259	K562	blood:	n/a	chr19:44281830-44281844 chr19:44281821-44281835
45	EP300	chr19:44281372-44282240	SK-N-SH	brain:	n/a	chr19:44281830-44281844 chr19:44281821-44281835
46	ELF1	chr19:44281564-44282270	GM12878	blood:	n/a	n/a
47	TCF3	chr19:44281840-44282034	GM12878	blood:	n/a	chr19:44281964-44281979
48	EP300	chr19:44281241-44282338	GM12878	blood:	n/a	chr19:44281830-44281844 chr19:44282264-44282278 chr19:44281821-44281835 chr19:44282268-44282277
49	RUNX3	chr19:44281123-44282371	GM12878	blood:	n/a	n/a
50	REST	chr19:44281521-44282437	HL-60	blood:	n/a	chr19:44281806-44281815

No.	Distal block	Cell Line	Cell type
1	chr19:44228240..44229809-chr19:44281869..44283736,2	K562	blood:
2	chr19:44091165..44093926-chr19:44279180..44281985,2	K562	blood:
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
ENSG00000104783	Chromatin interaction
ENSG00000105771	Chromatin interaction
ENSG00000167378	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	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56344893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56681946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62116961	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73048670	0.95[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
rs11879798	AC115522.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11879798	KCNN4	cis	Whole Blood	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44278200-44283800	Enhancers	Sigmoid Colon	Sigmoid Colon
2	chr19:44278800-44282000	Weak transcription	Esophagus	oesophagus
3	chr19:44278800-44283200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:44278800-44283400	Enhancers	Placenta Amnion	Placenta Amnion
5	chr19:44279000-44282600	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr19:44279200-44283000	Weak transcription	Right Atrium	heart
7	chr19:44279200-44283200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr19:44279400-44282800	Enhancers	Stomach Mucosa	stomach
9	chr19:44279600-44282000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr19:44279600-44282000	Weak transcription	NHDF-Ad	bronchial
11	chr19:44279600-44283000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:44279800-44282800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:44279800-44283400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr19:44279800-44283600	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr19:44279800-44283600	Weak transcription	Small Intestine	intestine
16	chr19:44280200-44283000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:44280400-44282400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr19:44280400-44282400	Flanking Active TSS	GM12878-XiMat	blood
19	chr19:44280400-44282800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr19:44280600-44282400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:44280600-44282800	Enhancers	Placenta	Placenta
22	chr19:44280600-44283200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:44280600-44284200	Enhancers	NHEK	skin
24	chr19:44280800-44282000	Weak transcription	Lung	lung
25	chr19:44280800-44282400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr19:44280800-44282400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:44280800-44283600	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr19:44280800-44284200	Weak transcription	Gastric	stomach
29	chr19:44280800-44284800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:44280800-44285800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr19:44281000-44282000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr19:44281000-44282400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr19:44281000-44282400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr19:44281000-44282400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr19:44281000-44283400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:44281000-44284600	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr19:44281200-44282000	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr19:44281200-44282000	Enhancers	Hela-S3	cervix
39	chr19:44281200-44282400	Enhancers	H9 Cell Line	embryonic stem cell
40	chr19:44281200-44282400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:44281200-44282400	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr19:44281200-44282400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:44281200-44282400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr19:44281200-44282400	Flanking Active TSS	K562	blood
45	chr19:44281200-44283400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:44281200-44283800	Enhancers	NH-A	brain
47	chr19:44281200-44284400	Enhancers	HUVEC	blood vessel
48	chr19:44281200-44285600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:44281400-44282200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr19:44281400-44282400	Enhancers	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links