Variant report

Variant	rs4968309
Chromosome Location	chr17:45300218-45300219
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45266341..45268368-chr17:45299147..45300680,2	K562	blood:
2	chr17:45298890..45301217-chr17:45302235..45305116,3	K562	blood:
3	chr17:45290405..45293270-chr17:45298817..45300612,2	K562	blood:
4	chr17:45298839..45301217-chr17:45302235..45304685,3	K562	blood:
5	chr17:45297983..45300898-chr17:45329772..45332242,2	K562	blood:

Variant related genes	Relation type
ENSG00000259207	Chromatin interaction
ENSG00000004897	Chromatin interaction
ENSG00000259753	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12946597	0.95[ASN][1000 genomes]
rs1515751	0.92[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[ASN][1000 genomes]
rs1515752	0.84[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.96[ASN][1000 genomes]
rs1713494	0.92[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs1713495	0.92[ASW][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs188799	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs2071438	0.84[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs221597	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs221598	0.87[ASN][1000 genomes]
rs221599	0.92[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs221602	0.91[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs3785875	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs701982	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs764792	0.92[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs8071382	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs858673	0.88[ASN][1000 genomes]
rs858679	0.92[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap]
rs938904	0.83[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4968309	SOST	cis	cerebellum	SCAN
rs4968309	NMT1	cis	cerebellum	SCAN
rs4968309	DBF4B	cis	parietal	SCAN
rs4968309	SKAP1	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45288400-45302000	Weak transcription	HSMM	muscle
2	chr17:45295600-45301800	Enhancers	Fetal Intestine Small	intestine
3	chr17:45296400-45304000	Enhancers	Stomach Mucosa	stomach
4	chr17:45296400-45305000	Enhancers	Spleen	Spleen
5	chr17:45297800-45300800	Enhancers	Duodenum Mucosa	Duodenum
6	chr17:45297800-45302000	Weak transcription	Gastric	stomach
7	chr17:45298000-45301200	Strong transcription	HSMMtube	muscle
8	chr17:45298200-45300400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr17:45298200-45300400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr17:45298200-45300600	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr17:45298200-45302000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr17:45298400-45302200	Weak transcription	NH-A	brain
13	chr17:45298400-45307000	Weak transcription	Fetal Lung	lung
14	chr17:45298400-45307400	Weak transcription	Fetal Brain Female	brain
15	chr17:45299000-45301000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr17:45299200-45300400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr17:45299200-45301800	Enhancers	Fetal Intestine Large	intestine
18	chr17:45299200-45302000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr17:45299200-45302800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr17:45299400-45300800	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr17:45299400-45301000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr17:45299600-45300400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr17:45299600-45302600	Enhancers	Left Ventricle	heart
24	chr17:45299600-45304200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr17:45299800-45301400	Enhancers	Lung	lung
26	chr17:45299800-45302000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr17:45299800-45302000	Weak transcription	Small Intestine	intestine
28	chr17:45300000-45300600	Genic enhancers	Fetal Heart	heart
29	chr17:45300000-45301600	ZNF genes & repeats	K562	blood
30	chr17:45300000-45302800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr17:45300000-45304000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr17:45300200-45300400	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr17:45300200-45300800	Enhancers	Adipose Nuclei	Adipose
34	chr17:45300200-45300800	Enhancers	Placenta	Placenta
35	chr17:45300200-45300800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr17:45300200-45300800	Enhancers	Hela-S3	cervix
37	chr17:45300200-45300800	Enhancers	NHDF-Ad	bronchial
38	chr17:45300200-45300800	Enhancers	Osteobl	bone
39	chr17:45300200-45301000	Genic enhancers	Fetal Muscle Leg	muscle
40	chr17:45300200-45301000	Enhancers	Right Ventricle	heart
41	chr17:45300200-45301000	Enhancers	NHEK	skin
42	chr17:45300200-45301400	Enhancers	Right Atrium	heart
43	chr17:45300200-45301400	Enhancers	HMEC	breast
44	chr17:45300200-45302600	Enhancers	HUVEC	blood vessel
45	chr17:45300200-45304000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr17:45300200-45304200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links