Variant report

Variant	rs496427
Chromosome Location	chr11:64838173-64838174
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64834740..64837631-chr11:64837991..64841500,4	K562	blood:
2	chr11:64836229..64838255-chr11:64883552..64886004,2	MCF-7	breast:
3	chr11:64822195..64823771-chr11:64836946..64839026,2	K562	blood:
4	chr11:64806813..64809943-chr11:64836893..64838926,3	MCF-7	breast:
5	chr11:64832286..64836236-chr11:64837835..64842573,5	MCF-7	breast:
6	chr11:64832014..64834014-chr11:64836154..64838250,2	K562	blood:
7	chr11:64838165..64840293-chr11:64846529..64848257,2	MCF-7	breast:
8	chr11:64820733..64823695-chr11:64836946..64838617,2	K562	blood:
9	chr11:64826169..64829330-chr11:64836105..64838372,3	MCF-7	breast:
10	chr11:64836894..64839909-chr11:64862538..64865060,3	MCF-7	breast:
11	chr11:64780520..64784503-chr11:64834796..64838390,5	MCF-7	breast:
12	chr11:64811497..64814543-chr11:64837067..64840304,3	MCF-7	breast:
13	chr11:64837451..64840290-chr11:64841461..64843514,2	MCF-7	breast:
14	chr11:64837909..64840950-chr11:64880960..64884927,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000213465	Chromatin interaction
ENSG00000174276	Chromatin interaction
ENSG00000255173	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000146670	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000168061	Chromatin interaction
ENSG00000168060	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11227118	0.96[ASN][1000 genomes]
rs11227120	0.96[ASN][1000 genomes]
rs11231929	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1196048	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2282498	0.96[ASN][1000 genomes]
rs36057475	0.96[ASN][1000 genomes]
rs3802936	0.90[ASN][1000 genomes]
rs3862374	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs475089	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs477539	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs484182	0.81[ASN][1000 genomes]
rs489489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs498636	0.86[ASN][1000 genomes]
rs532373	0.83[ASN][1000 genomes]
rs534236	0.83[ASN][1000 genomes]
rs548150	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559644	0.83[ASN][1000 genomes]
rs564966	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs653111	0.85[ASN][1000 genomes]
rs6591869	0.83[ASN][1000 genomes]
rs7943007	0.96[ASN][1000 genomes]
rs947799	0.90[EUR][1000 genomes]
rs9971546	0.90[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
rs496427	SNX15	cis	Muscle Skeletal	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64822400-64850800	Weak transcription	Esophagus	oesophagus
2	chr11:64833600-64845600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr11:64834000-64838400	Enhancers	GM12878-XiMat	blood
4	chr11:64834200-64850600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:64834400-64845000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr11:64834600-64843000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:64834600-64846200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:64834800-64843000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:64834800-64843200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:64834800-64843400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr11:64834800-64843400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:64834800-64844800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:64834800-64845000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:64834800-64847800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:64835000-64843000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr11:64835000-64843200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr11:64835000-64843400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:64835200-64844000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr11:64835400-64843200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr11:64835400-64845000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:64835600-64843200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr11:64835800-64843000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr11:64836000-64843000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr11:64836600-64843200	Weak transcription	Fetal Stomach	stomach
25	chr11:64837000-64840000	Weak transcription	Spleen	Spleen
26	chr11:64837000-64843200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:64837000-64843200	Weak transcription	NHEK	skin
28	chr11:64837200-64843400	Weak transcription	K562	blood
29	chr11:64837200-64844000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:64837400-64843400	Weak transcription	Fetal Thymus	thymus
31	chr11:64837400-64843600	Weak transcription	Fetal Intestine Small	intestine
32	chr11:64837400-64843800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr11:64837400-64844800	Weak transcription	Hela-S3	cervix
34	chr11:64837400-64848000	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr11:64837600-64839800	Weak transcription	A549	lung
36	chr11:64837600-64843200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr11:64837600-64843200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr11:64837600-64845000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:64837600-64845600	Weak transcription	Fetal Intestine Large	intestine
40	chr11:64837800-64843200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr11:64837800-64845000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr11:64837800-64845400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr11:64837800-64846800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:64837800-64850800	Weak transcription	Pancreas	Pancrea
45	chr11:64838000-64839400	Weak transcription	HepG2	liver
46	chr11:64838000-64844200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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