Variant report

Variant	rs11652439
Chromosome Location	chr17:45924358-45924359
allele	A/G
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45923661..45925474-chr17:45958248..45959760,2	K562	blood:
2	chr17:45924109..45925732-chr17:45935306..45937324,2	K562	blood:
3	chr17:45924201..45927115-chr17:46047307..46049661,2	K562	blood:
4	chr17:45920176..45925286-chr17:46018429..46022644,7	MCF-7	breast:
5	chr17:45920242..45924382-chr17:45959879..45966158,9	MCF-7	breast:
6	chr17:45924111..45929589-chr17:45940263..45947435,9	MCF-7	breast:
7	chr17:45923698..45927608-chr17:45971618..45975136,4	K562	blood:
8	chr17:45917469..45920388-chr17:45922918..45925733,3	MCF-7	breast:
9	chr17:45922908..45925647-chr17:45983799..45986055,2	MCF-7	breast:
10	chr17:45921031..45932631-chr17:45970978..45975136,16	K562	blood:
11	chr17:45921830..45924511-chr17:46124880..46127547,2	MCF-7	breast:
12	chr17:45922247..45925799-chr17:45947598..45950911,3	K562	blood:
13	chr17:45923054..45925688-chr17:45927768..45931360,5	K562	blood:
14	chr17:45922247..45924447-chr17:45948700..45950911,2	K562	blood:
15	chr17:45915230..45925590-chr17:45966201..45976437,35	MCF-7	breast:
16	chr17:45922488..45924994-chr17:45961129..45963501,2	MCF-7	breast:
17	chr17:45923146..45930414-chr17:45970842..45976007,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000141295	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000264243	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000108439	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1005655	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11079795	0.93[ASN][1000 genomes]
rs11079796	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11650289	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11650536	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16948401	0.91[ASN][1000 genomes]
rs16948590	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16948722	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3809869	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4794203	0.82[EUR][1000 genomes]
rs701984	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72833426	0.85[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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908573	chr17:45858487-45956073	Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv908574	chr17:45876022-45930584	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv517880	chr17:45887951-45933341	Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11652439	SCRN2	Cis_1M	lymphoblastoid	RTeQTL
rs11652439	OSBPL7	cis	Thyroid	GTEx
rs11652439	SCRN2	cis	Whole Blood	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45918800-45924600	Weak transcription	Spleen	Spleen
2	chr17:45919200-45928000	Weak transcription	Right Atrium	heart
3	chr17:45921000-45924600	Weak transcription	Pancreas	Pancrea
4	chr17:45921000-45927200	Weak transcription	A549	lung
5	chr17:45921200-45926000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr17:45922000-45925400	Bivalent Enhancer	Fetal Muscle Leg	muscle
7	chr17:45922000-45925600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr17:45922600-45927600	Weak transcription	Hela-S3	cervix
9	chr17:45923200-45925400	Bivalent Enhancer	Fetal Lung	lung
10	chr17:45923400-45925400	Bivalent Enhancer	Fetal Thymus	thymus
11	chr17:45923600-45924600	Weak transcription	Lung	lung
12	chr17:45923600-45925400	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr17:45923600-45925600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr17:45923800-45924400	Enhancers	NHEK	skin
15	chr17:45923800-45924600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr17:45923800-45924800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:45923800-45924800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr17:45923800-45925200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
19	chr17:45923800-45926000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
20	chr17:45923800-45926400	Weak transcription	K562	blood
21	chr17:45924000-45924400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr17:45924000-45924400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr17:45924000-45924400	Bivalent Enhancer	NH-A	brain
24	chr17:45924000-45924600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr17:45924000-45924600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr17:45924000-45925000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
27	chr17:45924000-45925000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr17:45924000-45925000	Bivalent Enhancer	Right Ventricle	heart
29	chr17:45924000-45925200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
30	chr17:45924000-45925200	Genic enhancers	Placenta	Placenta
31	chr17:45924000-45925800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
32	chr17:45924000-45925800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
33	chr17:45924000-45925800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr17:45924000-45925800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr17:45924000-45926000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
36	chr17:45924000-45926200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
37	chr17:45924200-45924400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr17:45924200-45924400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr17:45924200-45924400	Bivalent Enhancer	Fetal Brain Male	brain
40	chr17:45924200-45924400	Flanking Active TSS	HMEC	breast
41	chr17:45924200-45924600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr17:45924200-45924800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
43	chr17:45924200-45924800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr17:45924200-45924800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
45	chr17:45924200-45924800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr17:45924200-45925000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
47	chr17:45924200-45925000	Bivalent Enhancer	Esophagus	oesophagus
48	chr17:45924200-45925200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
49	chr17:45924200-45925200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr17:45924200-45925400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--

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