Variant report

Variant	rs9915028
Chromosome Location	chr17:45927491-45927492
allele	G/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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45927242..45929769-chr17:46017796..46019388,2	MCF-7	breast:
2	chr17:45926861..45929500-chr7:5568593..5570213,2	MCF-7	breast:
3	chr17:45924111..45929589-chr17:45940263..45947435,9	MCF-7	breast:
4	chr17:45923698..45927608-chr17:45971618..45975136,4	K562	blood:
5	chr17:45912259..45914443-chr17:45925886..45928377,3	MCF-7	breast:
6	chr17:45925951..45927687-chr17:45928711..45930678,2	K562	blood:
7	chr17:45921031..45932631-chr17:45970978..45975136,16	K562	blood:
8	chr17:45927380..45931249-chr17:45931939..45938449,12	K562	blood:
9	chr17:45927036..45931880-chr17:45931939..45936922,11	K562	blood:
10	chr17:45912279..45914440-chr17:45926481..45928555,2	K562	blood:
11	chr17:45925187..45928793-chr17:46033650..46037470,3	MCF-7	breast:
12	chr17:45923146..45930414-chr17:45970842..45976007,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000075624	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000264243	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000108439	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	0.89[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	0.96[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	1.00[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]
rs9897598	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9903904	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9904503	0.83[EUR][1000 genomes];0.86[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
rs9915028	SCRN2	cis	Stomach	GTEx
rs9915028	SCRN2	cis	Esophagus Muscularis	GTEx
rs9915028	SCRN2	cis	Muscle Skeletal	GTEx
rs9915028	SCRN2	Cis_1M	lymphoblastoid	RTeQTL
rs9915028	SCRN2	cis	Esophagus Mucosa	GTEx
rs9915028	SCRN2	cis	lung	GTEx
rs9915028	SCRN2	cis	Skin Sun Exposed Lower leg	GTEx
rs9915028	SCRN2	cis	Whole Blood	GTEx
rs9915028	SCRN2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45919200-45928000	Weak transcription	Right Atrium	heart
2	chr17:45922600-45927600	Weak transcription	Hela-S3	cervix
3	chr17:45924200-45928000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr17:45925200-45927800	Weak transcription	Gastric	stomach
5	chr17:45925400-45927600	Weak transcription	Pancreas	Pancrea
6	chr17:45925800-45927800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr17:45925800-45927800	Weak transcription	Right Ventricle	heart
8	chr17:45925800-45928000	Weak transcription	Lung	lung
9	chr17:45926400-45929000	Flanking Active TSS	Placenta	Placenta
10	chr17:45926600-45927800	Flanking Active TSS	HMEC	breast
11	chr17:45926600-45930000	Bivalent Enhancer	Fetal Thymus	thymus
12	chr17:45926800-45928200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr17:45926800-45928200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
14	chr17:45927000-45927600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr17:45927000-45927600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
16	chr17:45927000-45928000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr17:45927200-45927600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
18	chr17:45927200-45927600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr17:45927200-45927600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr17:45927200-45927600	Enhancers	Colonic Mucosa	Colon
21	chr17:45927200-45927600	Enhancers	A549	lung
22	chr17:45927200-45927600	Enhancers	K562	blood
23	chr17:45927200-45927800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr17:45927200-45927800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
25	chr17:45927200-45927800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr17:45927200-45927800	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
27	chr17:45927200-45927800	Bivalent Enhancer	HepG2	liver
28	chr17:45927200-45928000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
29	chr17:45927200-45928200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
30	chr17:45927200-45928200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
31	chr17:45927200-45928200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr17:45927200-45928200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr17:45927200-45928200	Flanking Active TSS	NHEK	skin
34	chr17:45927200-45928400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr17:45927200-45928400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
36	chr17:45927200-45929600	Enhancers	Spleen	Spleen
37	chr17:45927400-45927600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
38	chr17:45927400-45927600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
39	chr17:45927400-45927600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr17:45927400-45927600	Bivalent/Poised TSS	Small Intestine	intestine
41	chr17:45927400-45927800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
42	chr17:45927400-45927800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr17:45927400-45927800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr17:45927400-45927800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
45	chr17:45927400-45927800	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
46	chr17:45927400-45928000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
47	chr17:45927400-45928000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr17:45927400-45928000	Bivalent Enhancer	Stomach Mucosa	stomach
49	chr17:45927400-45928400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
50	chr17:45927400-45928800	Active TSS	Esophagus	oesophagus

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