Variant report

Variant	rs1630903
Chromosome Location	chr15:57849243-57849244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11856	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439291	0.86[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12439292	0.91[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1620315	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1620402	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[ASN][1000 genomes]
rs1623697	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs1626448	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1666572	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1666573	0.90[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1690316	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1690317	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1690318	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17820431	0.91[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17820437	0.91[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17820449	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17820461	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17820467	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1908189	0.95[ASN][1000 genomes]
rs1908191	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1908192	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131730	0.85[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2131731	0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2131733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270487	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2635389	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2922231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2922232	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932208	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932209	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934418	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3742963	0.91[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs3742964	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4774960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4774961	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4774962	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55916627	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55952634	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56362917	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59368768	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66802357	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67336499	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7166305	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7171354	0.87[EUR][1000 genomes]
rs7171360	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8038795	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937248	0.91[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv904255	chr15:57790436-57907574	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1630903	CCNB2	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57837800-57853000	Weak transcription	Colon Smooth Muscle	Colon
2	chr15:57840800-57849400	Enhancers	Fetal Muscle Leg	muscle
3	chr15:57844600-57852200	Weak transcription	HepG2	liver
4	chr15:57844600-57859000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:57844800-57857400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr15:57845200-57852400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:57845200-57857600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:57846200-57852400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:57846800-57861400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:57847000-57854600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:57847200-57853400	Weak transcription	NHEK	skin
12	chr15:57847200-57854400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:57847400-57852200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr15:57847600-57851800	Weak transcription	Liver	Liver
15	chr15:57847600-57852200	Weak transcription	A549	lung
16	chr15:57847600-57852200	Weak transcription	HMEC	breast
17	chr15:57847600-57853400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:57847600-57854400	Weak transcription	Pancreas	Pancrea
19	chr15:57847600-57859200	Weak transcription	Right Ventricle	heart
20	chr15:57847800-57850200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:57847800-57852000	Weak transcription	Stomach Mucosa	stomach
22	chr15:57847800-57852400	Weak transcription	Fetal Intestine Large	intestine
23	chr15:57847800-57852400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr15:57847800-57852600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr15:57847800-57853600	Weak transcription	Fetal Stomach	stomach
26	chr15:57847800-57859000	Weak transcription	Gastric	stomach
27	chr15:57847800-57859200	Weak transcription	Ovary	ovary
28	chr15:57847800-57859200	Weak transcription	Right Atrium	heart
29	chr15:57848000-57852400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:57848200-57849400	Enhancers	Fetal Muscle Trunk	muscle
31	chr15:57848200-57851000	Weak transcription	NH-A	brain
32	chr15:57848600-57852200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr15:57848600-57852200	Weak transcription	Hela-S3	cervix
34	chr15:57848800-57852200	Weak transcription	Fetal Heart	heart
35	chr15:57849000-57852200	Weak transcription	HUVEC	blood vessel
36	chr15:57849200-57849400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links