Variant report

Variant	rs498636
Chromosome Location	chr11:64807541-64807542
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:64807448-64807811	HepG2	liver:	n/a	n/a
2	HCFC1	chr11:64807321-64809595	Hela-S3	cervix:	n/a	n/a

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64806669..64810557-chr11:64862016..64868359,8	K562	blood:
2	chr11:64793282..64795774-chr11:64807101..64811680,5	K562	blood:
3	chr11:64793697..64796700-chr11:64806482..64812345,9	MCF-7	breast:
4	chr11:64780179..64786029-chr11:64807067..64810211,7	MCF-7	breast:
5	chr11:64787088..64789367-chr11:64807052..64810027,2	MCF-7	breast:
6	chr11:64807090..64809871-chr11:64850334..64853304,4	MCF-7	breast:
7	chr11:64780338..64782626-chr11:64806994..64809935,3	K562	blood:
8	chr11:64545248..64547245-chr11:64807000..64808581,2	MCF-7	breast:
9	chr11:64798286..64800870-chr11:64805869..64808336,2	K562	blood:
10	chr11:64807050..64811411-chr11:64876533..64881108,6	MCF-7	breast:
11	chr11:64644663..64647408-chr11:64807363..64809566,4	MCF-7	breast:
12	chr11:64806537..64808623-chr11:64852176..64854982,2	K562	blood:
13	chr11:64645854..64647856-chr11:64806233..64808621,2	K562	blood:
14	chr11:64807534..64810713-chr11:64846257..64849828,3	MCF-7	breast:
15	chr11:64806772..64810496-chr11:64862454..64866792,5	K562	blood:
16	chr11:64806463..64808805-chr11:64815100..64817067,2	K562	blood:
17	chr11:64806835..64808889-chr11:64875130..64876967,2	K562	blood:
18	chr11:64806821..64808860-chr11:64936413..64939146,2	K562	blood:
19	chr11:64793793..64795353-chr11:64806843..64809654,4	MCF-7	breast:
20	chr11:64793389..64797015-chr11:64806765..64809007,6	K562	blood:
21	chr11:64805658..64811611-chr11:64862545..64865451,9	MCF-7	breast:
22	chr11:64692132..64694352-chr11:64806387..64808974,2	K562	blood:
23	chr11:64804480..64810811-chr11:64850224..64856247,12	K562	blood:
24	chr11:64806998..64808499-chr11:64948414..64950755,2	MCF-7	breast:
25	chr11:64806922..64809393-chr11:64883452..64886674,3	MCF-7	breast:
26	chr11:64807098..64808802-chr11:64850233..64851800,2	K562	blood:
27	chr11:64806644..64812839-chr11:64862132..64865938,9	MCF-7	breast:

No data

Variant related genes	Relation type
SAC3D1	TF binding region
ENSG00000110047	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000014216	Chromatin interaction
ENSG00000174276	Chromatin interaction
ENSG00000168060	Chromatin interaction
ENSG00000254501	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000254614	Chromatin interaction
ENSG00000068971	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000204710	Chromatin interaction
ENSG00000255173	Chromatin interaction
ENSG00000146670	Chromatin interaction
ENSG00000110025	Chromatin interaction
ENSG00000269038	Chromatin interaction
ENSG00000162300	Chromatin interaction
ENSG00000270775	Chromatin interaction
ENSG00000168066	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10897543	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11227118	0.83[ASN][1000 genomes]
rs11227120	0.83[ASN][1000 genomes]
rs11231929	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196048	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2282498	0.83[ASN][1000 genomes]
rs36057475	0.83[ASN][1000 genomes]
rs3802936	0.81[ASN][1000 genomes]
rs3862374	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs477539	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs484182	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs489489	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs496427	0.86[ASN][1000 genomes]
rs532373	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs534236	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs548150	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs559644	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs564966	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs598241	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs653111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6591869	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7943007	0.83[ASN][1000 genomes]
rs9971546	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv3324692	chr11:64806676-64811174	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs498636	SNX15	cis	Muscle Skeletal	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64795200-64808000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:64795400-64808000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:64795600-64808000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:64795800-64807800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr11:64795800-64807800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:64795800-64808000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:64795800-64808000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:64796000-64807600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr11:64796000-64807800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr11:64796000-64807800	Weak transcription	Fetal Kidney	kidney
11	chr11:64796000-64808000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr11:64796200-64807800	Weak transcription	Small Intestine	intestine
13	chr11:64796200-64807800	Weak transcription	A549	lung
14	chr11:64796200-64807800	Weak transcription	HMEC	breast
15	chr11:64796200-64807800	Weak transcription	HUVEC	blood vessel
16	chr11:64796200-64807800	Weak transcription	NHEK	skin
17	chr11:64796200-64808000	Weak transcription	Osteobl	bone
18	chr11:64796400-64807600	Weak transcription	Fetal Brain Male	brain
19	chr11:64796400-64807800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr11:64796600-64807600	Strong transcription	Fetal Intestine Small	intestine
21	chr11:64796800-64808000	Strong transcription	Fetal Stomach	stomach
22	chr11:64798400-64807800	Strong transcription	Fetal Intestine Large	intestine
23	chr11:64798400-64807800	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr11:64798600-64807600	Strong transcription	Brain Germinal Matrix	brain
25	chr11:64798600-64807600	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr11:64798600-64807800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:64798800-64807600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:64798800-64807600	Strong transcription	Rectal Smooth Muscle	rectum
29	chr11:64799000-64807600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:64799000-64807600	Strong transcription	Right Ventricle	heart
31	chr11:64799600-64807600	Strong transcription	Brain Angular Gyrus	brain
32	chr11:64800400-64808000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr11:64801200-64807600	Strong transcription	Fetal Brain Female	brain
34	chr11:64803600-64807800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr11:64804600-64807600	Weak transcription	Fetal Heart	heart
36	chr11:64804600-64807600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr11:64805000-64807600	Strong transcription	Brain Cingulate Gyrus	brain
38	chr11:64805000-64807600	Strong transcription	Brain Hippocampus Middle	brain
39	chr11:64805000-64807600	Strong transcription	Brain Substantia Nigra	brain
40	chr11:64805200-64807600	Strong transcription	Brain Anterior Caudate	brain
41	chr11:64805800-64807600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:64805800-64807600	Weak transcription	Primary T cells from cord blood	blood
43	chr11:64805800-64807600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr11:64806000-64807600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:64806000-64807800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr11:64806200-64807600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:64806200-64807600	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr11:64806200-64807800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr11:64806200-64807800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr11:64806200-64807800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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