Variant report

Variant	rs8078688
Chromosome Location	chr17:45919869-45919870
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:45919784-45920132	K562	blood:	n/a	n/a
2	SMC3	chr17:45917380-45919880	SK-N-SH	brain:	n/a	chr17:45918729-45918739
3	FOXA1	chr17:45919695-45920110	HepG2	liver:	n/a	n/a
4	FOXA1	chr17:45919861-45920190	HepG2	liver:	n/a	n/a
5	FOXA1	chr17:45919778-45920220	HepG2	liver:	n/a	n/a
6	CTCF	chr17:45917785-45920041	A549	lung:	n/a	chr17:45918728-45918738 chr17:45918726-45918735 chr17:45918726-45918739

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45917528..45920214-chr17:46032690..46035678,3	MCF-7	breast:
2	chr17:45919624..45921396-chr17:45944468..45946269,2	K562	blood:
3	chr17:45919558..45921234-chr17:45966853..45967975,40	MCF-7	breast:
4	chr17:45918850..45921918-chr17:45964837..45968341,4	K562	blood:
5	chr17:45918236..45922252-chr17:45971224..45975227,6	K562	blood:
6	chr17:45916146..45920179-chr17:45971137..45974158,6	K562	blood:
7	chr17:45918878..45920635-chr17:45927299..45929830,2	MCF-7	breast:
8	chr17:45918706..45921396-chr17:45943154..45946269,3	K562	blood:
9	chr17:45915230..45925590-chr17:45966201..45976437,35	MCF-7	breast:
10	chr17:45919859..45920596-chr17:46095215..46095744,2	MCF-7	breast:
11	chr17:45906340..45909429-chr17:45918735..45922764,3	K562	blood:
12	chr17:45919839..45921158-chr17:45966971..45968605,11	MCF-7	breast:
13	chr17:45914114..45922201-chr17:45959661..45964608,11	MCF-7	breast:
14	chr17:45917897..45920844-chr17:46033567..46035986,3	MCF-7	breast:
15	chr17:45913484..45922782-chr17:45969196..45975741,24	MCF-7	breast:
16	chr17:45917724..45920476-chr17:46044625..46046608,2	MCF-7	breast:

No data

Variant related genes	Relation type
SCRN2	TF binding region
ENSG00000159111	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000266821	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000141294	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]
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]
rs9897598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs8078688	SCRN2	cis	Whole Blood	GTEx
rs8078688	SCRN2	cis	Adipose Subcutaneous	GTEx
rs8078688	SCRN2	cis	Esophagus Muscularis	GTEx
rs8078688	SCRN2	Cis_1M	lymphoblastoid	RTeQTL
rs8078688	SCRN2	cis	Skin Sun Exposed Lower leg	GTEx
rs8078688	SCRN2	cis	Muscle Skeletal	GTEx
rs8078688	SCRN2	cis	Esophagus Mucosa	GTEx
rs8078688	SCRN2	cis	Stomach	GTEx
rs8078688	SCRN2	cis	lung	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45918600-45922600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:45918800-45920600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr17:45918800-45921000	Enhancers	Rectal Mucosa Donor 29	rectum
4	chr17:45918800-45921200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr17:45918800-45921200	Enhancers	Colonic Mucosa	Colon
6	chr17:45918800-45921200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr17:45918800-45922400	Enhancers	Fetal Intestine Large	intestine
8	chr17:45918800-45924600	Weak transcription	Spleen	Spleen
9	chr17:45919000-45920000	Enhancers	Brain Anterior Caudate	brain
10	chr17:45919000-45920200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr17:45919000-45920200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr17:45919000-45920200	Enhancers	Primary T cells fromperipheralblood	blood
13	chr17:45919000-45920200	Weak transcription	NHDF-Ad	bronchial
14	chr17:45919000-45920400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr17:45919000-45920400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr17:45919000-45920400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr17:45919000-45920400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr17:45919000-45920400	Weak transcription	Brain Angular Gyrus	brain
19	chr17:45919000-45920600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr17:45919000-45920600	Weak transcription	Osteobl	bone
21	chr17:45919000-45920800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr17:45919000-45920800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr17:45919000-45920800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr17:45919000-45920800	Enhancers	Fetal Stomach	stomach
25	chr17:45919000-45921000	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr17:45919000-45921000	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr17:45919000-45921000	Enhancers	A549	lung
28	chr17:45919000-45921200	Flanking Active TSS	HepG2	liver
29	chr17:45919000-45921600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr17:45919000-45921800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr17:45919000-45921800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr17:45919000-45922000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr17:45919000-45922200	Enhancers	Fetal Intestine Small	intestine
34	chr17:45919200-45920200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr17:45919200-45920400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr17:45919200-45920400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr17:45919200-45920400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr17:45919200-45920400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:45919200-45920400	Weak transcription	Fetal Brain Male	brain
40	chr17:45919200-45920400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr17:45919200-45920600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr17:45919200-45920600	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr17:45919200-45920600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr17:45919200-45920600	Weak transcription	Fetal Heart	heart
45	chr17:45919200-45920600	Enhancers	Dnd41	blood
46	chr17:45919200-45920800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr17:45919200-45920800	Weak transcription	Esophagus	oesophagus
48	chr17:45919200-45921600	Weak transcription	Right Ventricle	heart
49	chr17:45919200-45921800	Weak transcription	Lung	lung
50	chr17:45919200-45928000	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links