Variant report

Variant	rs73323378
Chromosome Location	chr17:46044912-46044913
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:46044803-46045659	U87	brain:	n/a	n/a
2	FOS	chr17:46044890-46045748	MCF10A-Er-Src	breast:	n/a	chr17:46045561-46045571 chr17:46045550-46045561 chr17:46045561-46045571 chr17:46045548-46045559 chr17:46045561-46045571 chr17:46045296-46045305 chr17:46045561-46045571 chr17:46045550-46045561
3	RCOR1	chr17:46044490-46045839	IMR90	lung:	n/a	n/a
4	MAX	chr17:46044508-46045845	A549	lung:	n/a	n/a
5	POLR2A	chr17:46044729-46044921	A549	lung:	n/a	n/a
6	SP1	chr17:46044633-46045817	A549	lung:	n/a	chr17:46045316-46045326 chr17:46045316-46045326
7	SIX5	chr17:46044805-46045695	A549	lung:	n/a	n/a
8	MAX	chr17:46044805-46045813	A549	lung:	n/a	n/a
9	FOSL1	chr17:46044883-46045964	HCT-116	colon:	n/a	chr17:46045561-46045571 chr17:46045561-46045571 chr17:46045548-46045559 chr17:46045561-46045571 chr17:46045296-46045305 chr17:46045561-46045571 chr17:46045550-46045561
10	POLR2A	chr17:46044758-46045665	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:45917724..45920476-chr17:46044625..46046608,2	MCF-7	breast:
2	chr17:46039634..46045111-chr17:46046533..46049867,10	K562	blood:
3	chr17:46031321..46037809-chr17:46043555..46050276,13	K562	blood:
4	chr17:46040813..46045111-chr17:46046677..46049654,4	K562	blood:
5	chr17:46043414..46046355-chr17:46124548..46126704,2	MCF-7	breast:
6	chr17:46030056..46036320-chr17:46039939..46045055,5	K562	blood:

Variant related genes	Relation type
CDK5RAP3	TF binding region
ENSG00000167183	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17617010	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793741	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794318	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4794333	0.91[ASN][1000 genomes]
rs8082043	0.88[ASN][1000 genomes]
rs886444	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs73323378	SCRN2	cis	Esophagus Muscularis	GTEx
rs73323378	SCRN2	cis	Skin Sun Exposed Lower leg	GTEx
rs73323378	SCRN2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
2	chr17:46027200-46047200	Weak transcription	Spleen	Spleen
3	chr17:46027600-46047400	Weak transcription	Right Ventricle	heart
4	chr17:46027600-46047600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr17:46028000-46047400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr17:46028000-46047600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:46030200-46045800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr17:46035000-46047400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr17:46036000-46047200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr17:46036600-46047800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr17:46036800-46047400	Weak transcription	Thymus	Thymus
12	chr17:46037800-46047400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr17:46037800-46047400	Enhancers	Fetal Intestine Small	intestine
14	chr17:46037800-46047800	Enhancers	Fetal Intestine Large	intestine
15	chr17:46038000-46046400	Weak transcription	K562	blood
16	chr17:46039600-46047600	Weak transcription	Primary T cells from cord blood	blood
17	chr17:46042800-46045000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr17:46042800-46045800	Enhancers	Ovary	ovary
19	chr17:46042800-46047800	Weak transcription	Small Intestine	intestine
20	chr17:46043000-46045800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr17:46043000-46045800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr17:46043000-46046400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr17:46043000-46047800	Enhancers	Pancreas	Pancrea
24	chr17:46043000-46047800	Enhancers	Stomach Mucosa	stomach
25	chr17:46043200-46046400	Weak transcription	Gastric	stomach
26	chr17:46043400-46045000	Enhancers	Hela-S3	cervix
27	chr17:46043400-46045400	Enhancers	Placenta Amnion	Placenta Amnion
28	chr17:46043600-46045600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr17:46043600-46046000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr17:46043800-46045800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr17:46043800-46045800	Enhancers	HMEC	breast
32	chr17:46043800-46045800	Enhancers	NHDF-Ad	bronchial
33	chr17:46044000-46045000	Weak transcription	Colonic Mucosa	Colon
34	chr17:46044000-46045600	Enhancers	HepG2	liver
35	chr17:46044200-46045200	Weak transcription	HSMMtube	muscle
36	chr17:46044200-46047600	Weak transcription	Liver	Liver
37	chr17:46044400-46045600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr17:46044600-46045000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr17:46044600-46045000	Enhancers	Osteobl	bone
40	chr17:46044600-46045200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr17:46044800-46045000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr17:46044800-46045000	Enhancers	NH-A	brain
43	chr17:46044800-46045200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr17:46044800-46045200	Flanking Active TSS	NHEK	skin
45	chr17:46044800-46045400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr17:46044800-46045400	Enhancers	Colon Smooth Muscle	Colon
47	chr17:46044800-46045400	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr17:46044800-46045400	Enhancers	Lung	lung
49	chr17:46044800-46045400	Enhancers	HSMM	muscle
50	chr17:46044800-46045600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links