Variant report

Variant	rs9897598
Chromosome Location	chr17:45923496-45923497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:45923480-45923630	AG09319	gingival:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45920176..45925286-chr17:46018429..46022644,7	MCF-7	breast:
2	chr17:45920242..45924382-chr17:45959879..45966158,9	MCF-7	breast:
3	chr17:45917469..45920388-chr17:45922918..45925733,3	MCF-7	breast:
4	chr17:45922908..45925647-chr17:45983799..45986055,2	MCF-7	breast:
5	chr17:45921031..45932631-chr17:45970978..45975136,16	K562	blood:
6	chr17:45921830..45924511-chr17:46124880..46127547,2	MCF-7	breast:
7	chr17:45921785..45923529-chr17:45941412..45943127,2	K562	blood:
8	chr17:45922247..45925799-chr17:45947598..45950911,3	K562	blood:
9	chr17:45923054..45925688-chr17:45927768..45931360,5	K562	blood:
10	chr17:45922247..45924447-chr17:45948700..45950911,2	K562	blood:
11	chr17:45915230..45925590-chr17:45966201..45976437,35	MCF-7	breast:
12	chr17:45922488..45924994-chr17:45961129..45963501,2	MCF-7	breast:
13	chr17:45923146..45930414-chr17:45970842..45976007,11	MCF-7	breast:

No data

Variant related genes	Relation type
SCRN2	TF binding region
ENSG00000108439	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000141295	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11079797	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16948424	0.86[EUR][1000 genomes]
rs16948662	0.98[EUR][1000 genomes]
rs2010952	0.86[EUR][1000 genomes]
rs34156395	0.88[EUR][1000 genomes]
rs59111282	0.88[EUR][1000 genomes]
rs62076106	0.86[EUR][1000 genomes]
rs6503875	0.98[EUR][1000 genomes]
rs7212099	1.00[EUR][1000 genomes]
rs7214694	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8078688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916798	0.86[EUR][1000 genomes]
rs9895764	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9896712	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9903904	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9904503	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9915028	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9897598	SCRN2	cis	Muscle Skeletal	GTEx
rs9897598	SCRN2	cis	Esophagus Muscularis	GTEx
rs9897598	SCRN2	cis	Skin Sun Exposed Lower leg	GTEx
rs9897598	SCRN2	cis	Adipose Subcutaneous	GTEx
rs9897598	SCRN2	cis	Stomach	GTEx
rs9897598	SCRN2	cis	Esophagus Mucosa	GTEx
rs9897598	SCRN2	Cis_1M	lymphoblastoid	RTeQTL
rs9897598	SCRN2	cis	Whole Blood	GTEx
rs9897598	SCRN2	cis	lung	GTEx

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

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	chr17:45920200-45923800	Enhancers	K562	blood
4	chr17:45920800-45923800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr17:45921000-45924600	Weak transcription	Pancreas	Pancrea
6	chr17:45921000-45927200	Weak transcription	A549	lung
7	chr17:45921200-45923800	Weak transcription	NHEK	skin
8	chr17:45921200-45926000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr17:45921800-45923600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr17:45921800-45923800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
11	chr17:45921800-45924200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr17:45922000-45924200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr17:45922000-45925400	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr17:45922000-45925600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr17:45922200-45923600	Enhancers	Placenta	Placenta
16	chr17:45922200-45923800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
17	chr17:45922600-45923600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr17:45922600-45923800	Weak transcription	HMEC	breast
19	chr17:45922600-45927600	Weak transcription	Hela-S3	cervix
20	chr17:45922800-45923600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr17:45923200-45923800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:45923200-45925400	Bivalent Enhancer	Fetal Lung	lung
23	chr17:45923400-45923600	Enhancers	Lung	lung
24	chr17:45923400-45923800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr17:45923400-45924200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr17:45923400-45924200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr17:45923400-45925400	Bivalent Enhancer	Fetal Thymus	thymus

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