Variant report

Variant	rs11669175
Chromosome Location	chr19:44289824-44289825
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	NFIC	chr19:44289521-44289900	ECC-1	luminal epithelium:	n/a	chr19:44289686-44289702 chr19:44289685-44289702
2	REST	chr19:44289311-44289863	PFSK-1	brain:	n/a	n/a
3	SMC3	chr19:44288534-44289891	SK-N-SH	brain:	n/a	chr19:44289636-44289650
4	MTA3	chr19:44288954-44289855	GM12878	blood:	n/a	n/a
5	CTCF	chr19:44289406-44289905	HCT-116	colon:	n/a	chr19:44289629-44289650 chr19:44289641-44289648 chr19:44289409-44289422 chr19:44289634-44289652
6	MAFK	chr19:44289433-44289858	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr19:44289106-44290134	A549	lung:	n/a	chr19:44289629-44289650 chr19:44289641-44289648 chr19:44289409-44289422 chr19:44289634-44289652
8	RAD21	chr19:44289226-44289941	MCF-7	breast:	n/a	chr19:44289632-44289651
9	RFX5	chr19:44289405-44289827	Hela-S3	cervix:	n/a	n/a
10	REST	chr19:44289255-44289847	A549	lung:	n/a	n/a
11	ZNF143	chr19:44289449-44289828	K562	blood:	n/a	n/a
12	TCF12	chr19:44288283-44289988	MCF-7	breast:	n/a	chr19:44288708-44288715
13	E2F6	chr19:44289135-44289890	A549	lung:	n/a	n/a
14	RAD21	chr19:44288143-44290075	HCT-116	colon:	n/a	chr19:44288672-44288682 chr19:44289632-44289651
15	RUNX3	chr19:44289374-44289824	GM12878	blood:	n/a	n/a
16	SIN3AK20	chr19:44288363-44289941	MCF-7	breast:	n/a	n/a
17	RAD21	chr19:44289349-44289887	ECC-1	luminal epithelium:	n/a	chr19:44289632-44289651
18	RCOR1	chr19:44289183-44289882	Hela-S3	cervix:	n/a	n/a
19	SIX5	chr19:44288889-44290032	A549	lung:	n/a	n/a
20	CTCF	chr19:44289133-44290124	HCT-116	colon:	n/a	chr19:44289629-44289650 chr19:44289641-44289648 chr19:44289409-44289422 chr19:44289634-44289652
21	RAD21	chr19:44289243-44289980	A549	lung:	n/a	chr19:44289632-44289651
22	JUND	chr19:44288496-44289825	A549	lung:	n/a	chr19:44288778-44288787 chr19:44288753-44288761 chr19:44288779-44288790 chr19:44288752-44288762 chr19:44288752-44288762 chr19:44288777-44288786 chr19:44288776-44288788
23	RAD21	chr19:44289070-44289986	HCT-116	colon:	n/a	chr19:44289632-44289651
24	POLR2A	chr19:44288341-44289840	HCT-116	colon:	n/a	n/a
25	BCL3	chr19:44289022-44289932	A549	lung:	n/a	n/a
26	TBP	chr19:44289385-44289835	Hela-S3	cervix:	n/a	n/a
27	TCF12	chr19:44287989-44289983	A549	lung:	n/a	chr19:44288708-44288715
28	MAX	chr19:44289339-44289850	MCF-7	breast:	n/a	n/a
29	YY1	chr19:44289354-44289838	GM12878	blood:	n/a	chr19:44289585-44289597 chr19:44289587-44289595
30	CTCF	chr19:44289405-44289871	GM12878	blood:	n/a	chr19:44289629-44289650 chr19:44289641-44289648 chr19:44289409-44289422 chr19:44289634-44289652
31	MYC	chr19:44289167-44289825	K562	blood:	n/a	n/a
32	RAD21	chr19:44289425-44289842	HepG2	liver:	n/a	chr19:44289632-44289651
33	RAD21	chr19:44289446-44289851	K562	blood:	n/a	chr19:44289632-44289651
34	REST	chr19:44289409-44289903	HL-60	blood:	n/a	n/a
35	GATA3	chr19:44289178-44289838	MCF-7	breast:	n/a	chr19:44289411-44289421
36	CTCF	chr19:44289393-44289866	K562	blood:	n/a	chr19:44289629-44289650 chr19:44289641-44289648 chr19:44289409-44289422 chr19:44289634-44289652
37	SP1	chr19:44288372-44289891	A549	lung:	n/a	chr19:44288721-44288734
38	JUN	chr19:44289060-44289849	K562	blood:	n/a	n/a
39	FOSL1	chr19:44288090-44289910	HCT-116	colon:	n/a	chr19:44288778-44288787 chr19:44288753-44288761 chr19:44288779-44288790 chr19:44288752-44288762 chr19:44288751-44288762 chr19:44288752-44288762 chr19:44288777-44288786 chr19:44288776-44288788
40	EBF1	chr19:44289511-44289858	GM12878	blood:	n/a	n/a
41	EP300	chr19:44289202-44289944	A549	lung:	n/a	n/a
42	CTCF	chr19:44289348-44289943	MCF-7	breast:	n/a	chr19:44289629-44289650 chr19:44289641-44289648 chr19:44289409-44289422 chr19:44289634-44289652
43	WRNIP1	chr19:44289428-44289856	GM12878	blood:	n/a	n/a
44	RCOR1	chr19:44289204-44289846	K562	blood:	n/a	n/a
45	CTCF	chr19:44289309-44289940	MCF-7	breast:	n/a	chr19:44289629-44289650 chr19:44289641-44289648 chr19:44289409-44289422 chr19:44289634-44289652
46	CREB1	chr19:44289269-44289833	A549	lung:	n/a	n/a
47	MYC	chr19:44289499-44289832	MCF10A-Er-Src	breast:	n/a	n/a
48	SMC3	chr19:44289327-44289862	GM12878	blood:	n/a	chr19:44289636-44289650
49	SMC3	chr19:44289236-44289848	K562	blood:	n/a	chr19:44289636-44289650
50	RAD21	chr19:44289132-44290011	A549	lung:	n/a	chr19:44289632-44289651

No.	Distal block	Cell Line	Cell type
1	chr19:44249057..44250070-chr19:44289173..44290085,5	K562	blood:
2	chr19:44248925..44250090-chr19:44289091..44290176,10	MCF-7	breast:
3	chr19:44248044..44248800-chr19:44289490..44290112,3	K562	blood:
4	chr19:44270617..44271581-chr19:44289245..44290116,2	MCF-7	breast:
5	chr19:43967500..43969727-chr19:44288135..44290383,3	MCF-7	breast:
6	chr19:44289645..44292572-chr19:44300661..44302875,2	MCF-7	breast:
7	chr19:44270260..44271258-chr19:44289187..44290070,3	K562	blood:
8	chr19:44256760..44265122-chr19:44281375..44290996,18	K562	blood:
9	chr19:44256245..44259869-chr19:44284477..44291035,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNN4-1	chr19:44289294-44290302	XLOC_013347

Variant related genes	Relation type
KCNN4	TF binding region
ENSG00000105771	Chromatin interaction
ENSG00000124466	Chromatin interaction
ENSG00000159871	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10404672	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10404692	0.85[AMR][1000 genomes]
rs10405457	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10421887	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10422990	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11665924	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11670158	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11671215	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12460161	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12463370	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12974061	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3760982	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760983	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760984	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802199	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802200	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60184524	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61138927	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[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
rs11669175	KCNN4	cis	Whole Blood	GTEx
rs11669175	AC115522.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44285400-44291400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:44287400-44291400	Enhancers	HMEC	breast
3	chr19:44288000-44290200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:44288400-44290200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr19:44288800-44290200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr19:44289400-44302600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:44289600-44290000	Enhancers	NHEK	skin
8	chr19:44289600-44290800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:44289600-44291000	Weak transcription	HSMM	muscle
10	chr19:44289600-44293000	Weak transcription	GM12878-XiMat	blood
11	chr19:44289600-44294800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr19:44289600-44295400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr19:44289800-44290400	Enhancers	Hela-S3	cervix
14	chr19:44289800-44290800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:44289800-44300800	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links