Variant report

Variant	rs16965650
Chromosome Location	chr15:44959132-44959133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr15:44958983-44959322	GM12878	blood:	n/a	n/a
2	SPI1	chr15:44958977-44959420	HL-60	blood:	n/a	n/a
3	STAT3	chr15:44958651-44959333	GM12878	blood:	n/a	chr15:44959127-44959138
4	CTCF	chr15:44959080-44959230	GM06990	blood:	n/a	n/a
5	TBP	chr15:44958431-44959454	GM12878	blood:	n/a	n/a
6	SPI1	chr15:44958709-44959530	GM12878	blood:	n/a	n/a
7	RCOR1	chr15:44958738-44959394	GM12878	blood:	n/a	n/a
8	CHD1	chr15:44958418-44959359	GM12878	blood:	n/a	n/a
9	CTCF	chr15:44958966-44959252	GM12878	blood:	n/a	n/a
10	SPI1	chr15:44959008-44959338	GM12891	blood:	n/a	n/a
11	SPI1	chr15:44959043-44959252	GM12878	blood:	n/a	n/a
12	SPI1	chr15:44958781-44959377	GM12891	blood:	n/a	n/a
13	ZNF384	chr15:44958868-44959363	GM12878	blood:	n/a	n/a
14	STAT1	chr15:44958830-44959415	GM12878	blood:	n/a	chr15:44959127-44959138
15	BHLHE40	chr15:44958482-44959293	GM12878	blood:	n/a	n/a
16	EBF1	chr15:44958674-44959360	GM12878	blood:	n/a	n/a
17	POLR2A	chr15:44958540-44959230	GM12878	blood:	n/a	n/a
18	SPI1	chr15:44958914-44959385	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:44958042..44960348-chr15:45002239..45005135,4	K562	blood:
2	chr15:44953988..44959855-chr15:44961562..44971881,15	K562	blood:
3	chr15:44953032..44957457-chr15:44958313..44962086,6	K562	blood:
4	chr15:44952988..44962373-chr15:45002018..45007307,26	MCF-7	breast:
5	chr15:44958863..44960885-chr15:45018628..45021313,3	K562	blood:
6	chr15:44955959..44959684-chr15:44967579..44969667,3	K562	blood:
7	chr15:44952188..44965604-chr15:45001074..45012963,51	K562	blood:
8	chr15:44953483..44956478-chr15:44958952..44962112,3	MCF-7	breast:
9	chr15:44958326..44960851-chr15:45019076..45021871,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPG11-5	chr15:44958590-44959217	NONHSAT042176

No data

Variant related genes	Relation type
SPG11	TF binding region
ENSG00000104133	Chromatin interaction
ENSG00000166710	Chromatin interaction
ENSG00000185880	Chromatin interaction
ENSG00000229474	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2555355	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs3759871	0.83[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs58231277	0.90[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	esv3386433	chr15:44654644-45037538	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	135 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16965650	LRRC57	cis	cerebellum	SCAN
rs16965650	SLC30A4	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44955800-44959200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:44955800-44959400	Weak transcription	Small Intestine	intestine
3	chr15:44956000-44959600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr15:44956200-44962800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:44956200-44968800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:44956400-44959200	Weak transcription	Right Ventricle	heart
7	chr15:44956400-44962200	Weak transcription	Placenta	Placenta
8	chr15:44956600-44959200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:44956600-44960600	Weak transcription	Spleen	Spleen
10	chr15:44957400-44961000	Weak transcription	Dnd41	blood
11	chr15:44958000-44959400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
12	chr15:44958000-44959600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr15:44958000-44959800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr15:44958200-44959600	Enhancers	Primary hematopoietic stem cells	blood
15	chr15:44958200-44959800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:44958200-44959800	Flanking Active TSS	GM12878-XiMat	blood
17	chr15:44958400-44959400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr15:44958400-44959400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr15:44958400-44959400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr15:44958400-44959400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:44958400-44959400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr15:44958400-44959600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr15:44958400-44959600	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr15:44958400-44959600	Enhancers	K562	blood
25	chr15:44958400-44959800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr15:44958400-44961200	Enhancers	Thymus	Thymus
27	chr15:44958400-44964800	Enhancers	Fetal Thymus	thymus
28	chr15:44958600-44959200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr15:44958600-44959400	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr15:44958600-44959400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr15:44958600-44959400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:44958600-44959600	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr15:44958600-44959600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr15:44958800-44959200	Active TSS	Primary T cells fromperipheralblood	blood
35	chr15:44958800-44959200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:44959000-44959200	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr15:44959000-44959200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr15:44959000-44959200	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr15:44959000-44959200	Enhancers	HepG2	liver
40	chr15:44959000-44959400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links