Variant report

Variant	rs564966
Chromosome Location	chr11:64850513-64850514
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:64849999-64850583	HepG2	liver:	n/a	n/a
2	E2F4	chr11:64850137-64852053	MCF10A-Er-Src	breast:	n/a	chr11:64851903-64851912
3	POLR2A	chr11:64850144-64853317	K562	blood:	n/a	n/a
4	POLR2A	chr11:64850226-64851919	H1-hESC	embryonic stem cell:	n/a	n/a
5	MXI1	chr11:64850510-64852620	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr11:64850343-64852171	PFSK-1	brain:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64849716..64853170-chr11:64935136..64939292,4	K562	blood:
2	chr11:64779637..64784611-chr11:64849890..64854060,9	K562	blood:
3	chr11:64849453..64851884-chr11:64947314..64948879,2	K562	blood:
4	chr11:64781269..64783468-chr11:64850067..64853147,4	MCF-7	breast:
5	chr11:64825921..64828072-chr11:64849835..64851535,2	K562	blood:
6	chr11:64807090..64809871-chr11:64850334..64853304,4	MCF-7	breast:
7	chr11:64849359..64854600-chr11:64874292..64883144,16	MCF-7	breast:
8	chr11:64779668..64784219-chr11:64849890..64854919,7	K562	blood:
9	chr11:64544180..64546675-chr11:64850197..64851760,2	MCF-7	breast:
10	chr11:64849716..64856389-chr11:64935136..64940419,9	K562	blood:
11	chr11:64644760..64647431-chr11:64850066..64853139,4	K562	blood:
12	chr11:64804480..64810811-chr11:64850224..64856247,12	K562	blood:
13	chr11:64849686..64855071-chr11:64883547..64886732,9	MCF-7	breast:
14	chr11:64849456..64854518-chr11:64877116..64882654,9	K562	blood:
15	chr11:64807098..64808802-chr11:64850233..64851800,2	K562	blood:
16	chr11:64849186..64851415-chr11:65269391..65271691,2	K562	blood:
17	chr11:64793687..64796323-chr11:64849331..64852233,3	K562	blood:
18	chr11:64850072..64852972-chr11:65026497..65029318,2	K562	blood:
19	chr11:64644462..64647222-chr11:64847025..64851524,4	MCF-7	breast:
20	chr11:64643788..64647961-chr11:64848883..64851896,4	K562	blood:
21	chr11:64793181..64796302-chr11:64849635..64852378,4	MCF-7	breast:
22	chr11:64793383..64797474-chr11:64849331..64856424,6	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZFPL1-1	chr11:64850435-64850895	l_490_chr11:64847717-64850895_adipose

No data

Variant related genes	Relation type
ZFPL1	TF binding region
CDCA5	TF binding region
ENSG00000251562	Chromatin interaction
ENSG00000014216	Chromatin interaction
ENSG00000014138	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000269038	Chromatin interaction
ENSG00000168060	Chromatin interaction
ENSG00000110025	Chromatin interaction
ENSG00000254501	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000204710	Chromatin interaction
ENSG00000168061	Chromatin interaction
ENSG00000255173	Chromatin interaction
ENSG00000174276	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000110047	Chromatin interaction
ENSG00000254614	Chromatin interaction
ENSG00000270775	Chromatin interaction
ENSG00000168066	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11227118	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[ASN][1000 genomes]
rs11227120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11231929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1196048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282498	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[ASN][1000 genomes]
rs2458298	0.80[CEU][hapmap]
rs36057475	0.99[ASN][1000 genomes]
rs3782094	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3802936	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs3825073	0.86[CHB][hapmap]
rs3862374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs475089	0.91[EUR][1000 genomes]
rs477539	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs484182	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs489489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs496427	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs498636	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs502333	0.84[JPT][hapmap]
rs532373	0.92[CEU][hapmap];0.81[ASN][1000 genomes]
rs534236	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs548150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs559644	0.81[ASN][1000 genomes]
rs566908	1.00[YRI][hapmap]
rs653111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6591869	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7943007	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[ASN][1000 genomes]
rs947799	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9971546	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897709	chr11:64772545-64870779	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv897710	chr11:64772545-64885445	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv897711	chr11:64772545-64900270	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs564966	SNX15	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64822400-64850800	Weak transcription	Esophagus	oesophagus
2	chr11:64834200-64850600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:64837800-64850800	Weak transcription	Pancreas	Pancrea
4	chr11:64840200-64850800	Weak transcription	Spleen	Spleen
5	chr11:64843600-64850600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:64845200-64850800	Weak transcription	Colonic Mucosa	Colon
7	chr11:64845400-64850600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:64846000-64850800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr11:64846000-64850800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr11:64846200-64850600	Weak transcription	Primary B cells from cord blood	blood
11	chr11:64846200-64850800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr11:64846200-64850800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr11:64846200-64850800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr11:64846200-64850800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr11:64846200-64851000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr11:64846200-64851000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr11:64846400-64850600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr11:64846400-64850800	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr11:64846600-64850800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr11:64846600-64850800	Weak transcription	Stomach Mucosa	stomach
21	chr11:64846800-64850800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:64846800-64850800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr11:64847200-64850800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:64847400-64850800	Weak transcription	Brain Angular Gyrus	brain
25	chr11:64847600-64850600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr11:64847600-64850600	Weak transcription	Fetal Brain Male	brain
27	chr11:64848200-64850600	Weak transcription	Placenta	Placenta
28	chr11:64848600-64850600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:64848600-64850600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr11:64848600-64850800	Weak transcription	Fetal Intestine Large	intestine
31	chr11:64849000-64851200	Transcr. at gene 5' and 3'	Dnd41	blood
32	chr11:64849200-64850800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr11:64849400-64850600	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr11:64849400-64850600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:64849600-64850600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr11:64849600-64851000	Flanking Active TSS	GM12878-XiMat	blood
37	chr11:64849800-64850600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr11:64849800-64850800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr11:64850000-64850600	Enhancers	Fetal Stomach	stomach
40	chr11:64850000-64850800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:64850200-64850600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr11:64850200-64850600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
43	chr11:64850200-64850600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr11:64850200-64850600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr11:64850200-64850600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr11:64850200-64850600	Enhancers	Duodenum Mucosa	Duodenum
47	chr11:64850200-64850600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr11:64850200-64850600	Active TSS	Fetal Brain Female	brain
49	chr11:64850200-64850600	Genic enhancers	Fetal Lung	lung
50	chr11:64850200-64850600	Weak transcription	Lung	lung

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